Yes! You can decide to advertise for example:
Rental 1 on all channels
Rental 2 on all channels except HomeAway
Rental 3 only on Booking.com
As you finish the "Get Connected" checklist for each website you want to work with, you will have 2 options "Connect my properties" (meaning all of them) or "Choose which properties to connect". If you click on the later you can choose which properties you'd like to activate on the channel.