Just to share a couple of general observations I've made from owning 25 or 30 bugs over the last 8 years (most of them were junk . . . and the rest were real pieces of $&^@!) . . .
1. Battery trays love to rust. It's what they do best. Unless you do something to protect the new pan from the effects of the battery it's going to rust out too. It's not real uncommon to hear about someone loosing a battery out of the bottom of their Bug.
2. Bug floor pans RARELY rust from the bottom. If you want to know the true condition of the pan you have to look under the carpet. I've seen pans that looked like new from the bottom and a couple of months later the seat fell through!
You also need to know that all floor pans are not created equal. The best ones will cost two or three times as much as a cheap one . . . and might be 4 or 5 times a thick! A cheap one will work, but won't hold up as long and the seat tracks on cheap pans are a joke. And yes they make full sides (just like the original), quarter pans (front halfs and backs of one side), patch pans for the battery tray, and if you look hard enough you can sometimes find patch sections for other areas of the pans.
If the rest of the floors are in pretty good shape, you might be better off patching the battery tray unless you have the time and money to do it right . . . remove the body, remove the old pans, clean up the tunnel, weld in new top of the line pans, seal all the seams, then prime, paint and undercoat the whole chassis. If you want to patch it, the best thing to do is buy a battery tray . . . it's just a small section of the full pan that covers the area that typically rust out. If you are good with a mig or tig welder and take your time marking, cutting fitting, welding and grinding, you can make the patch undetectable. Or, you can just cut out the rusted area and epoxy the new battery tray down on top of the old pan. Seal and paint it good and give it a good undercoating and it'll show from under the car, but it'll still be very functional. I've even patched them with fiberglass. It'll keep your battery off the ground, it won't rust, and it's quick and cheap . . . but it looks like $**t!
Bug-Me Videos has a Video on replacing the pans that everyone I've talked to who has watched it says is great. I think they show how to replace the pan without removing the body and how to do it right (remove the body) . . . it might show installing a patch in the battery tray, but I'm not sure.
I've replaced the passenger side pan in three cars and drivers side in one . . . I installed them all without removing the body and used pop rivets to hold them in. All of them were cheap pans too. One pair of pans I bought from JC Whitney set me back $72 (for both pans) including FedEx ground shipping. This kind of repair is a double edged sword . . . it's quick and cheap, doesn't require any special tools or skills and it's better than dragging your battery down the road. However, you can forget ever getting your seat to adjust (if you ever get it beat on to the joke of a seat track to begin with) . . . and plan on doing it right the next time you have to replace them. That'll probably be within 5 years.