**SOLVED- Sort of -**Using more than 2 inputs on Scarlett 6i6

My main interface is installed a rack case for an on-site recording Thursday.  I have a Karaoke singer session today so I thought I'd use my backup unit, a Scarlett 6i6.  But, I needed three inputs.  I ran the two (stereo) karaoke tracks to the two analog mic/instrument front panel inputs and a mic, via a ISA One preamp, to channel 3 on the rear.  I find there is no way to control the rear channels 3 to 6 in the Focusrite control program.  And, the only way to hear the mic on channel 3 is to enable echo in Sonar.  I had to hook up my main unit so I can do the session today (and probably tomorrow). 
 
The 6i6 is for sale. PM me
 

Different control.  I used to have a Saffire Pro 40 but the 6i6 has a very basic/limited control.  Although it has 6 inputs, it only shows and has controls for the two mic/line preamp inputs.  The others are "line" in and there is nothing in the control program for them.  I even updated to the latest control program but nothing new.

Your using the 6i6 a little bit different than what I would be doing.
I have never had to use Mix control for anything other than setting my buffers and toggling the line/instrument settings. 
 
First the rear 3/4 inputs are for line level so this is where the backing tracks would go.
Because they are line level they are not a problem for 90% of the things you would interface, like a synth, drum machine, DI or even a mike pre amp.
Reason is these devices all have there own level control so this is where you set the input level. There's no need for a second level control and this is standard for most interfaces as far as rear line inputs go. 
 
I have mine set for the input #3 receive signal from my Joe Meek pre amp and the #4 from my Radial Tone Bone acoustic guitar pre amp. I set Sonars record level by adjusting the output levels of those devices. 
The #1 input I use for other mikes, like my snare or guitar amp. The #2 is an XLR send from my Bass amp built in DI. 
 
I don't do large sessions any more but I also have the option of using the SPDIF 5/6 inputs via my Yamaha 01V. 
 
If I record my band I use my Tascam which has more inputs. 
 
 

I'll have to test that as I don't use the Scarlet's headphone system I use a small mixer. 
Both the Joe Meek and the Tone bone have extra outputs so those run to the mixer. The Guitar and bass amp I hear plenty loud enough from the amps. I do use a second mike on the amp to the mixer sometimes. 
I run the 3/4 output of the 6i6 to the mixer and I can dial in any cue mix this way. I also have a Lexicon effects unit on the loop of the mixer from the days of recording other people. I prefer dry.  
 
I found this set up is faster to dial in any balance. I think the Mix Control would do all this but I gave up after an hour the day I first hooked it up and have never returned to that idea. 
I would imagine your not hearing 3/4 using direct monitoring is 100% a Mix Control issue. 
 
As I understand it you can set up 4 different cue mixes with mix control, all would be direct monitoring. 
If I was recording clients still I guess I would have had to figure it out. 

Certainly a wise choice as myself I have no use for gear that doesn't work for me. 
I took back 2 Voice harmonizers before settling on the Voice live acoustic for that very reasons. 
I guess I'm just a grumpy old fart but if gear needs me to read a manual more than once it's down the road. And the Scarlett mix control qualifies as such. I will not be buying another Focusrite interface. I have actually gone back to using my Tascam us1641 right now on my main DAW and the 6i6 is teamed up with my Laptop. 
 
My Tascam has the Computer/Input mix control right on the front panel so does not suffer the need for a GUI mixer. I like hardware control of my gear as it's bad enough needing 2 monitors just for Sonar. Needing a 3rd just to have a mixer is stupid.  So my little Mackie mixer solved the problem of mix control for me. I have real knobs that I 100% understand what happens when you turn them and they are right there inches from my finger tips at all times.
And I can swap out my 2 interfaces with no difference to how Sonar see's things other than input 3/4 become 11/12 with the Tascam. My monitoring doesn't change. 
And not only that... There is way more headroom so therefore a cleaner sound overall... It can be LOUD if you need it to be. Interface headphone pre amps are wimpy at best. 

Yes it's nice to have 2 systems. one studio and one for mobile. As I just said I swapped duty and now use my Tascam for the studio and the Scarlett for mobile.   Reason is I am at this point not recording any bands. I've set up my laptop and once I put my parts down it will go to my partners house so he can record his parts, Banjo, vocals and a 12 string. He's retired so has lot's of time on his hands and will be good distraction for him learning how to record with a DAW. 
Curt is an amazing banjo player but we are both getting on and we need to document these old songs before we fade away :)  We have over 60 songs we will record. 
 
Are you going to look for a second interface? Possibly the Tascam 4x4?  I like the looks of it. 
http://tascam.com/product/us-4x4/specifications/
 
As you can see all 4 channels can be used for either, mike line or instrument. And it has the mix control on the front panel. 2x headphone out as well. 
 

Ha Ha, Wow I didn't anybody here was older than me..( 65)  I think you get the prize for that Jack ! 
But ya, we've been playing music together for over 30 years now. 
It was like this Circus act I saw once, The young people were all called the AMAZING such an such , the old guy was called the LEGENDARY. 
 
My Tascam us1641 headphone output is wimpy but quiet. 

Picked up a new Tascam 4X4.  Good enough for a "backup" unit that will mostly collect dust.