Actually with ISBoxer's FTL, the FTL is separated from the actual spell, so you can use any modifiers you like.

Just use the "Many new Mapped Keys" in the FTL DPS Keys key map and press the key combos you want to add (see http://isboxer.com/wiki/WoW:Quick_St...th_auto-assist)

If you're using modifiers and they're not working, it might be because the Hold option is enabled in whatever Key Map you're using, or perhaps that you checked "Use FTL Modifiers" instead of using the FTL Assist Me mapped key. Either way I wouldn't be able to tell you without seeing your configuration.