We went to WDW the first day that ME was unveiled (May 5). We didn't receive our ME tags in time, so we were told to just get our bags and go to check-in. That's exactly what we did. Just get on the shuttle and go down to the luggage carousel (you have to go there anyway b/c of the shuttle). Get your bags and go to the ME desk to check in. Then, carry your bags into the queue they tell you to go to. When you load the bus, the driver will put them in the storage bins. The driver will also unload for you when you get to the resort.
We were so glad that we had to deal w/our own luggage on May 5th b/c we talked to so many people who waited hours (not one or two -- but 10 to 12+) to get their luggage!!!
We're prob. going to use ME this July and plan on dealing w/our own luggage again -- just to be safe!
So, yes -- do not use the tags that they send you if you want to carry your own luggage to the bus!