SO i watched the videos and have a quick question, when using an FTL setup can I still use modifiers for keys that are not part of the setup or do I need to have no modifier keys bound at all?

I hope that makes sense.

For example i have my movement keys bound as a keymap where pressing W triggers Shift+W. My forward movement in game is bound to Shift+W. Does having a binding like that screw with a FTL setup?
No. You would not apply FTL modifiers to movement keys -- you specifically pick which keys you want FTL modifiers applied to. However, the keys you do want FTL modifiers applied to, you are limited to not using conflicting modifiers. If you have 5 or more characters, this generally means you reserve an entire key -- such as a Num key -- for an ability in the game (though you do not need to press that key yourself to activate it, you can use whatever key combination you want). Hope that made sense