Must be a common issue as Focusrites Mix control is also the most oddball mixer in all my years of using mixers I've ever had to wrap my head around. I'm just glad I don't need to use it. Like all of them, it is very powerfull IF you figure it out, lots you can/ could do with routing, but, why so unorthadoxed terms and what not. 

You asked about when I don't use TotalMix.

The answer is when I put the device in class compliant mode and record using Linux Ubuntu studio.

TotalMix is not supported on Linux. I have not tried to make it work on Linux.

In CC mode, you can pull up pre-saved configurations. For example, you can have the two preamps set to phantom, auto level engaged in the four inputs or not, as you prefer. You can let track gains work as stereo or mono.

So, once in the right configuration, I use the nob on the device to raise gains and output levels.

I'm not sure if this helps. I may only be confusing you. Still, that's the answer to your question.

Your nob is surely controlling something.

Open TotalMix, twist the nob, look for what changes.

I haven't read the documentation for the BabyFace, but I'll bet it is similar to the UCX.

Page 87 of the manual covers operation at the unit. This includes how to adjust gains and enable phantom.

batsbrew
5.3. Operation at the Unit
 
Operation at the unit in online mode (drivers installed under Windows and Mac OS X, PC mode chosen at the unit) covers the most useful actions and situations in daily operation. Clearly labelled buttons together with an intuitive operation scheme give direct access to volume, monitoring and setup.
 
Input Gains
The gains of all four analog inputs can be controlled directly by the big encoder knob. Use IN to select input 1/2 or 3/4, then push SELECT several times to step through left channel, right channel or both. The selected channel and amount of gain is shown by a single LED flashing in the left INPUT level meters. Turn the wheel to increase or decrease the gain. The three INPUT LEDs also show overload. Too hot levels will not be missed even if the level meter currently shows a quieter channel.
 
Output Volume
Select one of the three outputs via OUT, then turn the wheel. The current fader position of TotalMix FX (which moves in sync) is displayed via flashing single LEDs in the output level meter. The three output LEDs also show overload. Too hot levels will not be missed even if the level meter currently shows a quieter channel. 0 dB position: reduce the gain so that the yellow LED just turns off. OUT can also be reassigned to perform Speaker B switching in the Options/Key Commands dialog in TotalMix FX.
 
Output Balance
Select one of the three outputs via OUT, then hold down SELECT. The right level meters show two bars, lit up until the yellow LEDs. Turn the wheel to move the stereo image more to the left or right. This setting equals an adjustment of the PAN knob in a stereo hardware output of TotalMix FX, and indeed the knob in the software will move in sync. 10 User's Guide Babyface Pro © RME
 
DIM
Works on the hardware output defined as Main Output in TotalMix FX. Therefore the DIM LEDs will not be lit when stepping through the other two outputs. The applied attenuation is the one defined in TotalMix FX. DIM can also be used as hotkey for many other actions, among the switching to Speaker B or Talkback. Use the Options/Key Commands dialog in TotalMix FX to assign one of them to DIM.
 
Recall
Pushing DIM for two seconds sets the Main output volume to the value formerly saved for Recall. The Recall value can also be set directly at the unit by holding SET down for two seconds.

Thanks Bat... read it when I first got it, but obviously didn't absorb it... I will tonight.

gswitz
You asked about when I don't use TotalMix.

The answer is when I put the device in class compliant mode and record using Linux Ubuntu studio.

TotalMix is not supported on Linux. I have not tried to make it work on Linux.

In CC mode, you can pull up pre-saved configurations. For example, you can have the two preamps set to phantom, auto level engaged in the four inputs or not, as you prefer. You can let track gains work as stereo or mono.

So, once in the right configuration, I use the nob on the device to raise gains and output levels.

I'm not sure if this helps. I may only be confusing you. Still, that's the answer to your question.

Does shed light on your set up...thanks... and with regards to the knob, it doesn't seem to have any effect, even in TotalMix... but I seem to recall reading somewhere that the "gain" that you would see is minimal.
Dumb question, but I wonder if I can run the Baby in CC mode with Sonar and bypass TotalMix altogether...time to scour the RME forum I guess...Thanks again posters!

I do think CC mode works with Sonar, but it isn't quite as fast.

Might not be ASIO.

Personally, I only use cc mode when I must. Recording with an iPad. I did this just to say I had done it. Or recording with Linux.

Maybe this video will give you ideas...

https://youtu.be/lTHmki4VyfE

https://youtu.be/NVa3AyUNGuI

Totalmix is awesome once you get it figured out. A few things to remember that are not obvious... 
 
All Inputs are reflected into software on your computer/Sonar. What I mean by this, you don't select an "output" to affect what goes into the computer. Just select any input and the controls you see are what is going into the computer sans FX unless you have loopback on which I don't recommend to begin with.
 
So to set up to record in sonar it's as simple as selecting the inputs you are using and setting the gain/phantom power/etc. and set your input on the sonar track to that input and you're all set. 
 
To monitor via headphones (no latency) connected to the RME unit, or to use the main outs... Select the output you want to use. Click on the headphone output you want to use, once you click on it all the other settings/levels you see are what's going to that headphone output, your headphone mix. Then select the main outs, you may have to click the "assign" button to assign output channels to the mains, once you do that when you select the mains output what you see on the other channels is what is being sent to the mains. 
 
Click back and forth between the headphone output and the mains output. You'll see the other faders change as it changes from what is mixed into the heaphone output and what is mixed into the mains output. They can be completely independently mixed and have nothing to do with what goes into the computer. What goes into the computer is selected by selecting each input channel and manipulating it.
 
Hope that helps.  gabo

I just want to mention that unlike "hi-end golden USB cables", RME products have other reasons to be expensive.
Significant part of BF price is for TotalMix (precisely for the combination of the hardware and the software which implement it). 90 pages of the documentation explain EVERYTHING the device and Totalmix can do,  especially in case you immediately can test everything written (that was my problem before, but as you can see in my updated signature, no longer...).
 

gbowling
Totalmix is awesome once you get it figured out. A few things to remember that are not obvious... 
 
All Inputs are reflected into software on your computer/Sonar. What I mean by this, you don't select an "output" to affect what goes into the computer. Just select any input and the controls you see are what is going into the computer sans FX unless you have loopback on which I don't recommend to begin with.
 
So to set up to record in sonar it's as simple as selecting the inputs you are using and setting the gain/phantom power/etc. and set your input on the sonar track to that input and you're all set. 
 
To monitor via headphones (no latency) connected to the RME unit, or to use the main outs... Select the output you want to use. Click on the headphone output you want to use, once you click on it all the other settings/levels you see are what's going to that headphone output, your headphone mix. Then select the main outs, you may have to click the "assign" button to assign output channels to the mains, once you do that when you select the mains output what you see on the other channels is what is being sent to the mains. 
 
Click back and forth between the headphone output and the mains output. You'll see the other faders change as it changes from what is mixed into the heaphone output and what is mixed into the mains output. They can be completely independently mixed and have nothing to do with what goes into the computer. What goes into the computer is selected by selecting each input channel and manipulating it.
 
Hope that helps.  gabo

good synopsis there, gbowling....
 
this has been my experience as well.
 
once you realize that you can set up multiple mixes of what you hear, even multiple headphone mixes, and how to route the rme inputs to whatever, it gets easier.
 
the basics:
when you plug a mic in, and set the inputs in sonar, everything as far as the capture goes is in the totalmix, as far as levels, and even printing eq and delay, or not printing it but hearing it.
very cool.