You're in Command

If you cast You’re in Command targeting a token and that token leaves the battlefield, it ceases to exist. Why did you put a token in charge?

If you have a commander in the command zone as You’re in Command resolves, that card is no longer your commander. It remains in the command zone and can’t be cast.

If You’re in Command targets a creature that’s represented by multiple cards, each of those cards become your commander. The additional cost to cast them and combat damage dealt by them are tracked separately for each card. Damage dealt while they’re together representing one creature counts for each of those commanders.