Can i overwrite my vista install?

yes you can install vista on the same partition multiple times, it just moves the old files into backup folders which are easily found on your C: and no there wont be a choice on bootup.

It's just really dirty running, as there's so many duplicates of files.

I've done it a few times so I could back up some files and reformat.

If you were able to install vista without losing data, you wouldn't accomplish anything. Whatever your reason for wanting to format, the problem would still be there as any issues are caused by something interacting undesirably with your OS. If you have no access to a backup drive, I would suggest shrinking your current partition, creating a second one containing everything you want to backup, then formatting and reinstalling vista on the original.

The best way is to reformat.

windows will create a folder known as windows.old. it's annoying to have on your hard drive. that's why u should reinstall a fresh copy instead

Yes just chose to have it save your stuff and not delete it

the windows.old folder won't bother me,i can delete it right?

You can do a repair install. It will bring the system back to how it was when first installed, and you keep all your installed programs and files. Not the best way to do it, and you should back up any important files no matter what.