I think i see, so if i have FTL modifiers set up under my characters and I make a /cast Immolate macro, I can use the num1 key as the mapped key target. However I should not make, shift+Num1 do something else like open my bags in wow.
Correct. (Well, mostly -- Shift+Num 1 isn't a valid key binding anyway, but if you were comparing, say, ] versus shift+] then absolutely)

However, if you avoided using any of CTRL, SHIFT, or ALT as FTL modifiers, you CAN reuse a given key with that modifier. For example, if you are playing 5 characters and used: lctrl, rctrl, lctrl+lalt, lctrl+ralt, rctrl+lalt as modifiers, then you avoided using Shift, and you could use ] for an FTL key, and shift+] for something non-ftl (it may not work with FTL conditionals built into ISBoxer as currently implemented, because it's checking nomod on shift)