Basically you're asking how to have 2 different sets of rewrite rules working at once...
If you want to use custom rewrites then you'll need to start reading up on mod_rewrite and how to write the rules, it's not simple (not what you're asking)... which is why you've likely not received much of a response..
In theory, yes you could do it (most things are possible)... but you'd need to have some explicit understanding of how the rewrite rules work, where they need adjustment, where new additions need to be, and so on.... (or you could ask someone that has a very good knowledge of mod_rewrite)..
Option 1: Personally i'd suggest hiring someone who has some in-depth knowledge of mod_rewrite (if not only for peace of mind) to write the custom rules to work alongside the existing rules..
Option 2: The cheap alternative is to read the docs and start playing with the rules yourself (use a test install of course), like i do... :)
Option 3: Wait here patiently and hope someone offers up a solution..
Once you understand more of how mod_rewrite works, i think you'll be able agree there's more then a few ways you could do this, but each would require testing, testing.... testing and ....more testing.. (not something a forum volunteer is likely to do for you - sorry)..