1. This website (the For Sale or "BST" forum)
2. scottycameron.com- You can get certain "stock" headcovers there, the limited releases (sometimes) and if you send a putter for restoration or customization, I'm pretty sure you get more choices than you get from the "Accessories" section of the Studio Store.
Some covers (as you probably know) are way easier to get than others. The "stock" offerings (Studio Design, Circa 62, Studio Style) are much easier to come by than others. (You can get the Circa 62 directly from the cameron store) Limited editions, Circle-T's, Holiday designs, fan favorites (Hula-Girl, Shamrock, certain golf-Majors) are much harder to come by and can go for hundreds (or MORE).
I don't blame you for abandoning eBay as an option, I'm starting to hate them as well, and there are WAY too many fakes out there. Unless you know your source (and even still you take a risk) it's too easy to get ripped off.
Do a lot of homework and be patient, I see brand new headcovers on the BST forum all the time here, designs that you think are long gone will pop-up from time to time because someone is desperate for cash.
Good Luck!