Second quest will be pounding the forum on advice or if it's even possible on how to setup a patch specifically to match my analog (tones from my pedals/amp) setup. Is that the custom IR thing I've read about?
Just take it piece at a time:
Get the 4 cable method working with your amp (since this seems to be your main goal right now), and start feeling what effects work for you and tweaking them. It’s really the same as using pedals just in a virtual environment change the order of the effects just by drag and dropping into place. (I assume you are going to use the editor for PC/MAC) However !! You can keep your routing options simple or get very complexed for example Lets run the compressor or reverb or delay in parallel and way way more------.
For the 4 cable method the effects loop block is the center of you universe.
Also use your Axe Fx with some studio monitors get the feel of playing FRFR great for those 2:00AM ideas you just have to lay down. With FRFR the amp and cab blocks are the center of your universe.
Other things you can do: did you create an effects chain that you really like while hooked up to your amp using the 4 cable method?? Cool ! Keep that preset copy it to a different location on the Axe Fx delete the effects loop and add an amp block and cab block to use FRFR. And of course you can do the opposite.
Don’t worry about custom IR’ s right now you will find plenty of factory standard IR’s that sound great! I have allot of cab packs but still use some factory standards. Keep in mind with the Axe Fx you can shoot a impulse of your own cab using your own microphones, if your cab was very unique.
Advice (for what it is worth)
For now don’t depend on the Axe Fx for your gigs till you get better acquaint.
Just enjoy it and push yourself to learn it ask questions read the manual and so on.
During this process everything will fall into place and won’t be frustrating.
There is nothing as frustrating as being at a gig and have to alter something and not sure how to do it. And jump on your phone and post a “Help” message on the forum while at the gig. And YES ! This has happened in the past.
John