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As far as ISBoxer goes, would I just put Lightning Bolt and Shadow Bolt on key 1, and press either, with the non-active window doing the same (press 1), but at the target of the active window?
Yes, exactly
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I use a ton of modifier keys in my macro's.
A button will do one thing normally, another with Alt, another with Ctrl, another with Shift.
Can I still make a button do a ton of things depending on modifiers used.
Or will the FTL require that the modifiers chosen are exclusively for FTL ?
Yes, you can still make keys that do different things depending on the modifiers. For example, I like to use CTRL to control a different subset of characters -- maybe my healer wont DPS if I dont hold CTRL, but if I do it means everyone DPS. Or if I hold Alt it might do AE damage instead of single target). Stuff like that. I do these things by making additional Mapped Keys. You can look at the "FTL DPS Keys" Key Map in ISBoxer (from the wizard) for examples, and then make your own in a similar way.