MY collection is upto about 250-300, so what I do is uploaded all of them to one site first...once I got that established, I started taking those same pics - and added them to the other sites. It's taking a long time categorizing. FTP uploading is great tho, on a hi-speed connection.
I keep folders as well, one for accepted, one for denied - but only for my main site I upload to, which is BigStock. After that, Ill make a newer set of folders and archive the old ones. The older archived ones then get uploaded to the other sites. I even upload the denied images to other sites, because you never know. What's rejected at one site, is many times accepted at another site.
Right now I'm on
BigStock - 250 images
Shutterstock - 50+
Dreamstime - 72+
CanStock - just starting out
Fotolia - hundred of my images have been in their cue for about 8 days. I'm hoping on hearing something from them soon.
So far Dreamstime is doing very well, and shutterstock is selling like hotcakes (even tho they're only 20 cents per photo, the more downloads makes up for it)
So for me, Dreamstime and Shutterstock are about hand in hand, I make about 2 bucks a day on each site right now. Bigstock usually gives me .50 -1.50 a day.
I'm testing the waters, and eventuall I'll figure out which sites to concentrate more on, and which ones to diss. It's like that old saying tho - don't put all your eggs in one basket. Upload your images to as many sites as you have time to

What's the harm? It's all free, and it's only going to get you a little more income. Not really income, at least not in my case - but some play money!