Upload & Sell: Off
Yes, you can register large amounts of photos per fee (I don't know if there's a cap but I've registered 10,000 images in one registration) and yes to only needing proper naming of the files. In reality, you can register quarterly (which is what I do) since you have 90 days to register your work if an infringement happens. If it happens any time up to 90 days before you register you're covered (this is meant to cover editorial photographers where their images are generally used immediately). So 4 registrations per year and if you're infringed you have actual legal recourse. If you wait until 90 days, you can still register your images but from 90 days on if an infringement happens before it's received by the copyright office you negate your ability to register (not sure of the technicalities of this but it's probably to prevent a massive backlog of issues).
The paper work is a single form that is filled out online (you have to have an account with them which is in fact cheaper) or you can fill out the paper work long hand (fee is more). I have yet to be able to upload my images via the website but instead put all images as 400x600 lines on a DVD and ship them in with the # provided after filling out the online form and paying the online fee.
The only time consuming part is renaming and resizing the files but you could certainly rename for registration at import should you choose. The theory behind renaming your files is approximate to this:
photographer name_job name_date created_(insert actual date created)january12013_file name.jpg
All files in that job are named that with the file name changing. Then you switch jobs and:
And so on. At first it's a bit inundating but it quickly becomes second nature. Then you just bunch all the files together on one DVD and off it goes in the mail. Infringements suck. I just found another image of mine used by a big company online but I have yet to find the time to get at it. I will, but after the seasonal rush is done.