With pretty much the sole exception of the $5000 for villages, all other money collected should go to the account for things like you're saying.
We generally let the $5k go straight to the staff as a little thank you. In modern VC, 5k is pennies for most people, I know, but that was the old thinking.
Staff can choose to send the 5k to the Villagecraft account. All other payments, like the 100k mob protection payment, should already be going there. Using this money to fund things like events, prizes, building projects, etc, is a good idea.