Good to see you are making headway.
Re #1, MC has always been limited to two inputs(one stereo pair), and I believe that has carried into MC6.
However, it should see both mic/instruments or Line Inputs 3/4.
Check Edit>Preferences>Audio Devices.
You will probably see one pair of inputs highlighted and one pair greyed out.
This is MC limiting you. It is not an issue in the other Cakewalk versions.
ASIO is kind of funny, and instead of seeing Input 1/Input 2, you will probably see Input 1L and Input 1R. Note the L and R markings on the face of the FA66.
The Line inputs(3 & 4) will probably show as Input3L and Input3R This is normal behavior.
So, to record both mic inputs, you would set up something like this:
Audio track 1
Input-ASIO In 1L
Output-Master
 
Audio Track 2
Input-ASIO In 1R
Output-Master
 
If your latency is good enough, and you want to hear effects such as amp sims as you record, turn on Input Echo.
Arm and Record.
 
Re #2, Fade in/out is the same. Be sure you have the smart tool selected. Hover your cursor over the top right corner of the clip, and you should see the fade triangle. If the clip is too small, you may want to zoom in so you can position the cursor.
hth

Yessir, the wonderful thing about being old and learning new technology is you have fewer years of frustration ahead. With renewed patience I got the fade out function. Thanks!
I also have a SeaSound Solo EX that uses a COM port, if I can figure out how to make it work that should at least let me record two separate tracks at the same time would it not?

You may be recording stereo tracks, using both inputs on 1 track. Select left input in 1 track and right input in another track and you should be able to record 2 tracks simultaneously.

joyof60
I also have a SeaSound Solo EX that uses a COM port, if I can figure out how to make it work that should at least let me record two separate tracks at the same time would it not?

It looks like you might have the breakout box for that. It requires a companion PCI card(similar to the EMU0404 that you were using before). Among other things, it is very old, and even if you had all the parts, it probably wouldn't work with a new computer.
The FA66 is capable of providing multiple inputs.
You just need to set up your inputs as Greg and I have described.
Check out this thread:
http://forum.cakewalk.com/Volume-Signal-PathPart-1Recording-m1519608.aspx
Your tracks should look pretty much like tracks 4 and 5 toward the bottom of the first post.
This was done with an older version (Sonar Home Studio 6). The graphics are a little different, but the principle is the same. Ideally, you want two mono tracks.
You'll get it. These initial hurdles are the worst part.

Thanks do much guys, I have been seeing what you are describing with much confusion for a while, and now it kinda makes sense. I am connecting my piano/keyboard into the digital 'toslink' input on the FA66, so when I select my record ASIO option I select the SPDIF stereo option. Is that what negates me from being able to assign a different input to another track?
Ideally I will need to mic two guitars independently with two vocals as well as run the piano stereo. The FA66 touted itself as having 6 outs/ and 6 ins. I think from what I have been seeing is a boast of all available I/O options, line/digital/stereo etc. as if one could use them all concurrently. I've learned to look at the pictures of the products carefully.
Question here is, am I limited by the MC6 software therefore would benefit from changing to a higher end/different product? If so, could someone suggest which one? (There are sooooo many!) and would I indeed benefit from a hardware mixer to do what I need? I was trying to go "mixer less" with the FA66, but it appears that it has some limitations.
2) just a thought, do I have to use the AISO drivers? Would a configuration of the others be better suited?
Thanks again guys for the responses and patience with an old man that let technology pass him by! You all are so kind!
Robert, I will try the link and maybe improve my learning curve. I know the SeaSound was dated (one of the reasons I liked it : / ) but was not aware I needed a special card, I had tried to adapt it to USB (from the COM port) and the found a COM port on the Motherboard that just needed an adapter cable to bring it to the I/O panel. I hate to resign it to propping the door open (it's so pretty) but alas, live and learn. One more time, thank you all so much!!

1.  yes, you are limited to 2 inputs at a time with the MC line. If you need more you need to cross grade to the X3 series and even the lowest one will give you more inputs at the same time depending of course on the interface you choose
 
2.  If the interface is designed to use ASIO drivers, you should make every effort to set them up and adjust the settings if, and as needed to use the ASIO drivers as the company designed it to function.  In my case, I simply installed the ASIO drivers from disk and they ran smooth as glass. You can also check the interface company's website for the most recent and updated drivers.... some folks do need to update the drivers..... it varies depending on your system.
 
You are not prevented from using MME drivers with most decent interfaces but you generally end up with the same performance issues you had with the factory card since MME is not designed to work with them efficiently.

Thanks again guys! Herb, those (software X3s) that allow greater than two inputs, will they return the same number?
And the AISO drivers for the FA66 work fine I guess, I was just reading somewhere that (and I know I don't have the names right) the WPA or something is more useful in sending multiple seperate tracks. And really don't fully understand half of what I read. You guys here have given me more useable information than I have read anywhere. Y'all are indeed a great service!

The SONAR X3 series does not impose limits on track count.  WRT to driver mode, usually it is a good idea to test an interface by running all the drivers supplied by the manufacturer as some interfaces work better with one or the other. This is because the actual drivers vary from manufacturer to manufacturer.

My Focusrite Saffire only has 2 inputs, but up to 10 outputs (or 5 stereo pairs), and my SONAR Home Studio 6 can utilize those outputs. Probably SONAR X can, too. If the interface has multiple outputs, you should be able to use them with the X series. Most only have 2 outputs, so check the specs before you buy.
In the case of the Saffire, that's so you can use it to drive a surround sound speaker system if you want.
I think.

With X3, the limit on the number of tracks is more a function of the computer and the interface. The number of inputs and outputs on the interface will all be recognized with X3.
 
Currently, with MC, you get 2 inputs. They can be 1 stereo or 2 mono inputs. Normally, the way I work, it's one mono track at a time.