I would say, in general, to avoid USPS flat-rate boxes unless you are shipping something that is both small and heavy. You can still get priority shipping on your own packaging, and you can fit much more for less money (up to 13oz I think for $5.10 if you buy on Etsy). I can't even come close to getting 13 oz of my products into a small flat rate shipping box. :\
If you have enough sales volume, I would say definitely consider purchasing boxes in bulk. I have purchased from Papermart.com, which is pretty cheap per unit. I'm finding that the corners don't necessarily line up nicely, so I'm going to try another vendor next time. Uline is more expensive than several other places I've priced. TheBoxery.com seems to have very good prices, particularly on certain standard sizes. I haven't purchased from them yet, but my next box purchase, I will. I learned about them from someone else's recommendation in a forum discussion. :)
I'm not sure how bulky your quilts are - another thing to watch out for is the box dimensions. Once any side goes over 12", the prices go up significantly.
Good luck with your shipping!