I would definitely want to be notified prior to the order being filled. I like have the check boxes and also put comments specifying what my expectations are. I also like having the quantity available listed, but if I absolutely must have something, I will call or email first to make sure they have the quantity I require (especially long cuts as I prefer not to piece borders unless I have to). I would be open to suggestions for similar items to use in place of what I ordered.
A few months ago, I received a package I wasn't expecting. It was a backordered item from an order I placed 4 months prior! No warning, no asking if I still wanted it. There was no estimated date on their website. I thought it was discontinued. It wasn't worth the hassle of returning, so I kept it. But I have not ordered from there again. If you don't have it, say so. If you can give a resonably firm timeframe for backorders, please communicate it with the customer so we can make an informed decision.
It's good you are polling your potential customers...to me, it shows you care how we feel! Good luck! :)