I don't re-seed but simply seed everything I download until the torrent becomes inactive because it is removed from the site or until I no longer want to keep it. If I no longer want to keep it, I make sure that there are several seeders before deleting it and will make it freeleech if there aren't approximately five or more seeders.
I keep active torrent files in a folder as a backup as they've come in handy when changing computers or hard drives or when there's a problem with the torrent software. A few thousand torrent files shouldn't take up even 100 MB.
I do standardize the names of downloads I want to keep but only when they become inactive.
It's pretty easy to find what I want by sorting or searching even though all the downloads are in the same large folder on a hard drive so I don't find there is any need to put everything in folders. I will sometimes keep collections in the same folder and I do use some tags to help with sorting.
In your situation, the basic process is:
Change the name of the downloaded file back to the exact original name.
Move the downloaded file back into the correct folder so your torrent software (client) can find it.
Download the torrent file.
Add the torrent file to your torrent software.
The torrent client should then automatically verify the file data and start seeding.
If the torrent client can't find the file, you may not have renamed it correctly or you may have to tell it where to find it.