Database structure for a system with multisite
I would recommend keeping everything in one database. It will be easier to manage and administer. If you need to add more domains/clients, you can continue to use the existing instance of the database (no need for new installations). The records that are specific to certain domains/clients will need some kind of indicator. It could be as simple as an client_id field. Installed instances of the application should have their client_id (or multiple values, if they're allowed to search more than one dataset) in their configuration so that every query where it matters contains the proper client_id. 

A possible alternative to having applications configured so the know what to query would be to move that configuration into the database, maybe in a table like this:


portals_hotels
--------------
   portal_id
   client_id

sample data:

portal_id   | client_id
------------|----------
www.x.com   | www.a.com
www.y.com   | www.b.com
www.y.com   | www.a.com