should I use "copy newer" or "smart backup"?

[susieq]

I’m a newbie who purchased Super Duper in order to back up one external disk drive onto another one. I’m doing a full-length documentary film and have two external drives (one firewire and the other usb2) of 1TB each. I run Final Cut Pro on my Mac HD, but store all media, project files, etc. on one of the external drives. I want to use the second external drive purely for backup, so I made the firewire drive the source and the usb the destination drive. I selected the “copy newer” option because I was afraid that if I chose the “smart backup” option, and for some reason, a file got deleted from my source drive, Super Duper would delete the accidentally deleted file from the destination drive during the next backup, thus negating any advantages of backing up my files onto the second drive.

Is this a correct assumption?

If so, the problem is this: I had many of the same files on both drives when I started my backup this afternoon, so I figured that SD would only have to back up a few files that might have been newer on the source drive than on the destination drive. I also figured that the destination drive would end up with basically the same amount of disk space available as the source drive, as the files were pretty much the same.

It’s been 3 hours now and the program is still copying. Not only that, but it seems to have copied about 100GB of files onto the destination drive more than what is currently on the source drive. Can anybody explain what’s happening here? Should I have chosen “smart backup” instead of “copy newer”? And will it take another 3 hours for the next backup, or is this just a one-time thing?

Thanks