Platoons are specific to TB, and yes, if you platoon a character you can't use it for battles. Whether that means you need to get in early or not is really up to how your guild officers run things. Ideally they will ensure everyone has enough left to complete missions.
As for deploying, always deploy last, after you have done all of your missions. Once you deploy to a sector you cannot use that character in another sector. So the general flow should be: platoon characters, wait for all platoons to fill, do your missions, deploy where directed.
