Like Wendy said, the vases/containers/etc. are separate line items in your floral budget. The way to figure it out is that anything they cannot re-use you are buying, and anything they can is a rental item. Therefore, you buy the flowers and votives and you rent the vases/containers (btw-you can have them quote you for buying the vases/containers, but this is obviously pricey).
When deciding on my floral vendor, I got a quote from Disney and 2 outside vendors. While the format of each quote was a bit different, the vases/containers/etc. were always considered rental items.
I eliminated nearly all of my rental fees with Disney Floral (which I think are very high anyway) by bringing in all my own "glassware" - basically any vase/container/votive holder/etc. I bought everything at a local wholesale floral distributor, decorated them myself, and my parents drove all these fragile items down to Florida. Two days before the wedding, my DH dropped everything off at the Disney Event Group offices (which is where the Disney Floral team actually works). You can ship the items to these offices if driving is not an option for you, but not until (I think) 2 weeks before the event due to their limited storage space.
It was a bit of work on my part, but it lowered my floral bill by hundreds of dollars (I bought everything at significantly lower prices) and I got to keep a few as keepsakes. My Disney Floral rep was very receptive to the idea of me bringing in my own, she never balked once or tried to get me to keep the rental items. There were very minimal set-up fees for us, and the cost savings far outweighed these fees.
Here are some pictures (every glass item you see, other than food service items, I brought in myself):
BTW, I was not charged for floral foam or anything to keep the flowers alive because I gave them the containers 2 days in advance. I would never recommend trying to do this the day of the wedding; it would be far too much stress to try and set everything up yourself and I doubt Disney would even allow it.