Easy, but difficult. Haha, they won't have dex entries, (unless you hack the pokedex, there is a thread in R&D for that), which will cause the game to crash when caught. So, they have to be evolved or given to the character. I use them for some of the extra evolutions added in Gen IV.
However, everything else works fine. Except icons.... Those have to be properly and completely repointed or else it reverses all sprite changes you made. So, just repoint every thing you can that deals with them and you should be fine.