New user, praise and a few questions

For question 1, I've been using the RAM banks as my scratch pad for new sounds. All of the pre-loaded RAM sounds also exist in the ROM banks (somewhere, you'll have to go find them as they're scattered about), so don't worry about losing any pre-loaded RAM sounds. I did a full sysex backup before I started working with my TI2 kbd though, just in case I ever needed to go back to factory default.

Multi-mode is also very powerful, much more so than most other synths... the first 16 entries in the multi bank can each hold 16 complete patches (i.e., you select a patch in multi 0, slot 1, all the way up to multi 15, slot 16 and it becomes a duplicate of the patch you chose). All parameter adjustments you make to patches in those first 16 entries are held within the multi bank and do not affect the original patch at all. So in essence you have RAM A - D (128 slots each), plus Multi 0 - 15 (16 slots each), for a grand total of 768 user defined patches. Not too shabby eh?

Edit: I did assume you have a TI or TI2, as I've only worked with the TI2 in-depth.

2 --> If I understand correctly, as with all patch parameters, you change the arpeggio and store the patch on the same patch location (or a new one).
1 --> I have a method that I have devised over a long time and I am still perfecting it, and I guess anyone can make their own variation on it. The key element here is how do you naturally remember your patches? I usually say to myself "I want to use (or build upon) the same lead/pad/etc. sound I used in <put song/show name here>". So I learned that I shouldn't rely solely on the ability of the DAW to save a project's patches in the plugin memory of the project file. What I do is export a patch bank, carrying the song's name, and having all the project's used patches in locations that match their MIDI channel number in the project (places 1 thru 16). I also give them names that reflect their contribution: high-pad, aux-bass, etc. On the rare occasion that I overdub the Virus with an additional set of up to 16 sounds for the same song, I use same bank but places 101 thru 116 for the sounds from the overdub session. The same goes for live shows - I back up the Virus setup in a folder that clearly states the date and tour/show name. For that reason a rarely use the built in categories, as I frequently use sounds "not as intended", and I find the category list to be missing a few terms such as "brass" and "stab". The downside is that I end up with a lot of duplicates or near-duplicates, but then again, I don't use the VC browser's search function that much.
Hope this helps.