Awesome, folks, thanks!!
I've been poking and pushing through this stuff, and have just now successfully learned how to download my info from VanCity to YNAB and clean it up in there. It's kind of awesome -I was really surprised at how simple it was, and at how sophisticated YNAB was in handling it! When I reduce my accounts, and as YNAB also learns how I want everything done, it should end up totally doable.
I might stick with manual entries for outgoing, because that keeps me conscious, and info download for deposits. I think that gives me all the benefits of Mint, etc, with none of the risks (or bank crabbiness).
TrMama: That sounds like an effective balance/compromise, too. (I might do something like that. I actually prefer not to see what the investments are doing anyway.)