How do I mark days I am not available?

On your dashboard calendar, once. Block the days there and they close on every tour you run, so there is no need to go through each tour's availability and untick dates.

Time off is absolute: it applies whether or not you allow overlapping bookings, and it does not touch bookings that are already confirmed. If you need to get out of one of those, cancel the booking itself so the traveller is told and refunded.