But when you're making your SD card bootable for Magic Lantern are you still able to use that card to store footage? And if that's the case do I have to make all of my cards bootable to use Magic Lantern on all the cards?
Yes, you can still store footage on the card. And, yes, you need to make all your cards bootable and install ML to use ML each time you insert a new card. If you use a non-bootable (non-ML) card, then the camera simply reverts to its normal operation without all the ML features.