Upon getting the all clear that the dates you want are open and the rate is correct, you sign the contracts and make the deposit.
Typically count on 50% down of the charter rate to confirm a charter and then the final balance due 60 days out along with any extra expenses, such as the APA (Advanced Provisioning Allowance), which many yachts charge depending on the area of the world.
For some charters that are more than six months out, you may be able to pay 25% to confirm the charter and then a further 25% six months out depending on the yacht.