The fee can be assigned per transaction.  Those fees are included in the block that pools find, that's anything ever the 12.5 Bitcoin.  Pools/Miners choose the transactions that have the highest transaction fee payout to maximize the gains.

If someone else includes our transaction in their block, they get the 45000 Satoshis that was sent as the transaction fee with that transaction.  If no one does and we find the next block, that transaction is included if it is still unconfirmed, thus, we get our own 45000 satoshis in our next block, which ends up going back to our pockets.