You'll need to use last.fm for this, but when you start to use it it'll erase all of your non-last.fm listening stats in MusicBee and start fresh with only plays that are already in last.fm for tracks that it can match to your MB library. In other words, going forward, when you sync and there is a "new" (to last.fm) track played, the play count for that track will be set to 1. It doesn't erase tracks that aren't sync'd (as far as I remember from when I made the decision to do this) only ones that it matches from last.fm.
Then you'll scrobble everything from your iPhone listening and also your home listening.
I'm afraid there's no other way. You have to decide whether your current MB listening history is more important to you than having an automatic history going forward.
The good news is I haven't noticed any "messed up scrobbling info" or "tagging issues," and I've been on this sync system for a year.