Pokémon from a GBA game can be transferred into a DS game, once you get far enough in the DS game (beat the Elite Four?). But they can't go the other way; once a Pokémon goes from a GBA game to a DS game, it's gone for good. I haven't gotten far in the DS games at all; I play the games obsessively too, and got so hung up on the GBA games that I was never able to satisfactorily move on to the DS games, what with school and such things getting in the way.
Also, I'm not sure if you know this, but the GBA and DS games are completely incompatible with the earlier Game Boy games (Red, Silver, et al). You can, however, play FireRed, which is a remake of Red made for the GBA, with some added stuff, too, but without the low-tech charm of the original's graphics or music. But you'll be able to transfer your Pokémon into a DS game, so that's good.
I wish I had kept up with Pokémon. Battling and trading would be fun. I've got lots of good stuff to trade. Maybe I should start again.[/nerd]
"No self-respecting alien would let zombies beat them to the punch." - Warflyzor