I've multiboxed FFXI quite a bit, and it's awesome. I did 1 character per PC though so I'm not sure which application will work well for you. It should be fine and I didn't have any issues with Square.
The nice thing about the game is that multiboxing melee is totally doable and fun since when you assist and attack they can auto run to the targeted enemy and stick on them.

Some of the BEST combo's you can utilize are Dragoons, they stack INSANELY well. I played with 3 and it was ridiculous with the Wyvern heal. Each one would heal for 300+ at 5 mp per cast, and with any type of mana regen it's unlimited, the heals are spread out between each wyvern so they never pull aggro.

A ton of Black Mages and a Bard is also insane. ugh I'd go back to the game if I didn't love WoW so much