Newb looking for some (simple) answers
 

The original HD drive that I purchased with my MacPro is too small and is now making funny noises... Time to replace with a larger drive. Will SuperDuper copy all of my previous programs, files and OS from my Macintosh HD? It sounds like it will, but I would like to make sure before I start messing around with the boot drive. I have a lot of updates for apps and plug-ins that I do not want to loose (obviously). If I can do this with SuperDuper, will I need to re-register all of my programs or does it make an exact copy? Is it easy to make the new HD the boot drive (or does the Mac automatically look to drive bay 1 for the OS and boot from there?)

You'd basically do this as a backup and restore operation (or, if you put both disks in the MacPro, just a backup). Any "copy protected" applications (many video/music applications fall into this category) will need to be de-authorized and re-authorized on the new drive.

You'll need to properly partition the new drive as "GUID", using the "Mac OS Extended (Journaled)" as the format. Also, name the new drive the SAME as the original drive, and remove the old drive before starting up from the new one.

Thanks for the info
 

That is exactly what I was looking for, Thanks!