There are two stages to setting up your online booking deposits
What deposits are you going to take? Go to Settings -> Bookings -> Online Booking Deposits -> Toggle to Active
When will you take a deposit - you can set here the minimum time or minimum booking value required to trigger taking a deposit. If you leave these required value and required duration boxes blank, it will always take a deposit.
How much deposit will you take - you can take either a fixed amount or a percentage of the booking value. If you enter a value in both of these boxes, it will take whichever is the highest for a particular booking
Setting up your Stripe account for pay outs. Go to Settings -> Stripe -> Connect with Stripe. This will take you to a Stripe page to fill out details about your business and the bank account you want your payouts to go into.