I'm assuming you are using MDF for the plenum. Just about anything will work at this stage as long as it is spread over it all evenly. I have used yellow glue and contact cement with fine results. My first two plenums were glued to the base with TB and the latest is down with Contact cement. No problems with any of them. For sealer I've been using shellac for years. I just brush in a couple coats before I set the spoil board.
For your last question I don't quite get it. I have 8 zones with 1" or so between them and have no issues with appreciable loss of vacuum when not using all zones.