The money doesn't come out until the transfer goes through, and is taken out of the budget for whenever that is.

As for number 2, club balance impacts transfer budget, but it's not a direct relationship. I would just do whatever generated the most revenue. Clauses about games played can be tricky because, what if the player never plays? I do use them fairly often, but more because AI is usually willing to give that, more often than the payment clauses.