I believe the sync feature works both ways, so perhaps if you use folders to move messages around for archiving (to keep the inbox cleaned up on all devices with only important/current messages), the watch will remove the filed messages from the list (it's not instant, but I deleted a message in Outlook and a few minutes later it wasn't on the watch anymore). So that might be one way to keep things simpler on the watch. I don't think it's designed to be an archive/retrieval platform, at least I would never want to use such a tiny display for that. If I need to look something up, I pull out my phone at that point.
Another "solution" would be to forward all mail from each account to a 4th "watch-only account" that you create somewhere, and sync only that account on the watch, so when you delete messages on the watch only the "disposable" email account gets wiped. This may not be an option depending on security policies for your company/Exchange account (I would imagine most companies would forbid forwarding mail off-server).