You may add a breakage fee as a regular fee under your dashboard > Bookings > Taxes & Fees. In this way, the fee will be automatically applied to every booking. Set “Limit” to 1 day, for the fee to be charged only once per the whole stay. However, please, note that Hotel Booking only enables payment functionality, but does not manage it. This means, all the refunds (for the breakage fee, for ex.) should be made manually.
You may configure for a guest to pay 50% deposit for the made booking, under your dashboard > Accommodation > Settings > Payment Gateways > User Pays.