Scenes affect all blocks the same, whether it be an amp, cab, delay, compression, whatever; they all behave the same. Regarding your statement "use a different amp in a separate scene"... basically, you can have 4 amps in a preset (Amp1/X, Amp1/Y, Amp2/X, Amp2/Y). What I was saying... let's say you start with a new, simple, preset with 1 amp and you get the X side (Amp1/X) dialed in perfectly in Scene 1. Then you go to Scene 2 and you decide that now you want more gain on the amp. If you modify Amp1/X and add more gain, that will affect Amp1/X in Scene 2 AND Scene 1 (that is bad -- I used to do this all the time until I finally got the hang of it); actually, it will modify Amp1/X in ALL scenes. The ONLY things you can vary across scenes on blocks is the Active/Bypass state and the X/Y state. You can use the scene to use the "Y" side of the same amp, or you can bypass the entire amp. So, if you want a new/different or modified Amp block in scene 2, you have two choices, 1) modify Amp1/Y (not X) or 2) add a second amp block, Amp2. If you add a second amp block to scene 2, you will most likely want to BYPASS Amp1 in Scene 2. My rule of thumb is if I want to modify an existing Amp block, I use the X/Y feature. If I want a different amp model in a specific scene, I will add a second amp block and make sure the other amp is bypassed in that scene. The best approach is based on your style, the song, your workflow and what makes sense to you.
Since a picture is worth a thousand words, this should also be very helpful. It's an easy 2-3 page read that helped me get started with scenes.
http://www.fractalaudio.com/downloads/manuals/axe-fx-2/Axe-Fx-II-Scenes-Mini-Manual-1.02.pdf
Per this doc... "As of firmware version 9, every Axe-Fx II preset1 contains eight scenes.
Each scene stores the BYPASS setting for every block in the preset, the X/Y selection for those blocks that support it, the main level of the FX LOOP block, and the preset’s MAIN output level. Scene changes are seamless and instantaneous, with perfect spillover requiring almost no effort. Scenes can easily be selected from the front panel or with a MIDI foot controller such as the MFC-101."
Hope this helps.