Hi zexelgrifone,
1. Yes, if use method CopyTo and MoveTo, then do not need to use SaveDirectory anymore.
2. The temp file will save into your system temp folder, mostly is "C:\Windows\Temp". You can set property "TempDirectory" to change the temp folder location like uploader.TempDirectory="D:/sites/aspuploader/mytemp/". If you use method "Moveto" to save the file, then the temp file will be removed after saved.
3. It will overwrite the same name file. Method "MoveTo" and "CopyTo" allow you save the file as any name you need, so you can check your exists file names first, and compare with the upload files. you can refer to http://cutesoft.net/forums/thread/72358.aspx, it may help.
Regards,
Ken