If you're intending to do this I'd pick your guild carefully up front with this in mind. I dual-boxed from the beginning in WoW. And I ran 5-mans with 2 friends (one of whom also dual boxed). I've raided in 3 different guilds. None of them were interested in letting me dual-box during raids - even when we were having problems getting enough people. Part of this was, frankly, due to social issues. All of the guilds I ran with had complicated loot rules, where you earn points based on attendance, etc. How would that be handled for someone multi-boxing? How would the other players feel about that? Etc.

I quit doing raids around BC and loot is generally handled very differently now. It might be very different this time around. And it might not... It would be very interesting to get into a raiding guild dedicated to multi-boxing...