No. Currently, BedBooking allows you to connect one accommodation establishment from Booking.com with a single BedBooking account. If you want to connect several accommodation establishments from Booking.com, you must have an identical amount of accounts on BedBooking.
There is a alternative solution, that allows you to connect two accommodation establishments from Booking.com with a single account on BedBooking. You can connect a second accommodation establishment from BedBooking via iCalendar.