I use a cloud based Property Management System by name of Openhotel. (openhotel.com).
I don't recall exactly, but is is like $5.00/room/month. I have been with them for 6 years with very few complaints. I think they connect to airbnb, not sure.
I do believe you can enter the number of rooms you are giving OTAs to book. If you are using a giant calendar to record your booking on which is what it sound like, and you have 10 apartment available, only list 4 or 5 on the OTA. Then as you get a booking from anywhere, go into the OTA extranet and take on of the available rooms you gave them away. The other alternative is to find a decent Property Management System and a channel Manager. You enter the number of rooms you have into your PMS.
When a reservation comes in from one of the OTAs, that unit is subtracted automatically from your inventory so no one else including you can book it.