From everything I've been reading about the upgrade pricing for the new every two program and the Best Buy pre-order is that you should be able to use the discount there. Most best-buy mobiles have confirmed that they will honor the new every 2 program discount. Seeing as they are tied into the verizon system it should show up when they look at your account. (Stated by a best buy employee) But there have been a few that have stated that they don't, so to be 100% sure on that you should also call your local Best Buy and ask to make sure. Also from what I heard to pre-order from best buy, they are making you purchase a $50 gift card.
One of the big misconceptions right now is whether or not verizon is making you send in a mail in rebate for the $100. This is not the case. Upon receipt of purchase of the droid they are giving you the rebate in the form of a $100 debit card. Which if you order it off-line i am seeing that the rebate will be instant. So either Best Buy is getting all the debit cards and just combing the money or verizon is being nice to them and just giving them a lump sum after they report how many units are sold.