There should be no real difference between running the same macro from ISBoxer to running it through a key press bound to an ingame macro as far as I understand. The main advantage in setting up things in ISBoxer is that you can create a more flexible setup utilizing ATG and FTL mechanics as well as your team being much easier to tweak since you can, for example, edit all your locks at once rather than having to make the same changes in 3 separate game windows.

As far as splitting characters, there are ways. You can setup mapped keys for this exact purpose. However, they require premeditation. I.e. You need to know which characters you'll want to split and how, or just have a bunch of different keys for different situations.

I'm not aware of anyone currently doing a traditional setup and clearing raid bosses. Atleast one has been killed by tank-stacking groups (ie: all blood DK / all prot paladin). That's not to say it's not possible. More so that no one, to my knowledge, has really tried.

Finally I'll just suggest that you might end up needing more RAM. I cap my 16GB at times with 9 characters with not that much running in the background.