Replacing Macintosh HD

I'm having some problems with my main HD in my G5. I purchased a new drive and I'm currently using SuperDuper to backup/copy/clone from one to the other with the new drive connected via external USB drive case.
Am I correct in assuming that once this is done, I can simply replace the internal drive with the new drive?

My question in the other thread was pertaining more to SuperDuper - sorry for the confusion.
The problem with the old drive was that I couldn't repair permissions on it, ran a Verify Disk and it came back saying that I needed to repair the drive, however, the Repair Drive button was not active. I forget the exact error message, but my local Mac guy said it looks like the drive was starting to fail and I should backup/replace it asap.
So, I've done the clone/backup using SuperDuper (tried CarbonCopy Cloner, but it missed about 10GB of files) and just swapped it out with the old drive. Everything seems to be running fine - everything seems to be in place.
Is there anything I can/should do to make sure it's ok? Some kind of test perhaps?
If I reformat the old drive now, should it be ok to use as a backup? I've got a 2nd drive built in and all my data is on it with an external firewire drive of same size that SuperDuper backs up to every day. I'd like to do the same for the system drive now, but not sure if I should use the old internal (put it in a firewire case) or just scrap it and get a new one.

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