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I assume that no one has replied because no one has any idea as to what this means: "I have my first drive linking to my second drive, via aliases, so that I can actually drag and drop larger files on my first drive into my second drive for storage."
Since both drives can show up on the desktop, why cannot you just drag and drop files from your boot drive to the backup drive? And, if you use SuperDuper!, it is clear from the documentation, that it will erase your backup drive and then make the clone, so, as far as I can understand, you will loose your backups, and the aliases on your boot drive will now point to nothing. I can not imagine what will happen if you also have aliases on the boot drive that are the same name as real files on your boot drive, but I would assume that they would just be copied along with the files of the same name to the clone, but will no longer have any files to point to.
And I cannot imagine what Time Machine would do with the aliases, but I would fear that redundent recursion would fill up the Time Machine drive the first time Time Machine ran!
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