OK so you're not really a dummy
I was hoping someone could let me know if there are any problems that I should expect or any "tricks" I can use to avoid some confusion...
I can't really think of any "problems" you should expect other than the usual mismatch between your intuitive expectations and how the software manufacturer implemented their interface. Those are somewhat unpredictable and depend a lot on prior experience with other software packages and with knowledge in the subject (recording, that is). From three years on this board and observations of what seems to hang people up the most, I would suggest the following list of areas that cause some head-scratching:
(1) Basics of MIDI: what MIDI actually is and how it's used, where the sounds come from, what MIDI channels are, why the MIDI tracks need to be recorded to an audio track before you can include them in a stereo mix, etc..
(2) Audio inputs: line and mic inputs on soundcards, how to enable or disable piping some of what's passing through the soundcard to its audio recording input, how to set decent levels.
(3) The stereo issue, which you specifically asked about, and I'll talk more about in a second.
Also my mixer has stereo outputs so should I record on two tracks at a time?
In my mind, the only reasons for recording stereo tracks are (1) you are attempting to capture the vibe of a real place -- a great room or hall that has a fantastic natural reverberance; or (2) you have already put the mixing effort into getting, say, the MIDI tracks mixed the way you want, so when you render them to audio a single stereo track will suffice. I would even add that this second reason is bogus because it involves making mix decisions earlier than normal, and once you've recorded it to audio this way you're stuck with your premix, unless you want to redo it, in which case you would have better off all along recording each MIDI part to a mono track and mixing it like any of the other audio tracks...
The recording application is where you capture the stuff you want to record, part by part, and either mix it there on the computer, or send all the multiple tracks out to an external mixer for mixing. You want to be able to readily place any of the recorded parts wherever you want to in the stereo image. If the recorded parts are already in stereo, it it very difficult to pan them, because each part is already panned, and the effect of panning two tracks with different amounts of signal is somewhat complex and unpredictable. It is infinitely simpler to record mono tracks and then adjust their leftness and rightness by panning them in the stereo field.