OS X :: Using Time Machine With Carbon Copy Cloner?

As of today, I upgraded my iMac (and eventually my Macbook) to Snow Leopard. I used Carbon Copy Cloner to create a clone of my drive to my external (I did a clean install) and now that Snow Leopard is installed, I only want to put back on to my computer just certain files, such as a select selection of my documents, some of my iTunes library, etc. Given that I couldn't find that option in Migration Assistant, I just manually copied over what I wanted from the clone on my external. Still, I would like to keep a daily backup for my iMac's HD and that's where Time Machine comes in, but there's some questions I have before I do it: Given that my iMac's HD now has significant free space (as I only brought back, say, 10% of the stuff to my iMac from my external when I cloned on CCC), if I enabled Time Machine to back up my iMac's HD stuff, it wouldn't overwrite the 90% of stuff on my external with the 10% that's on my iMac's HD, would it?

For instance, I have about 20,000 songs on my external drive, but maybe have brought back only, say, 5,000 to my iMac (for now). Given that my iMac's iTunes Music folder shows 5,000 songs on it, when TM backs that up to my external drive, it won't overwrite the other iTunes Music folder which has the other 15,000, right? The same thing could be applied for documents, photos, etc. If not, how would TM deal with that? I would hope to avoid the other extreme, which are duplicate files/folders. I guess I just want to be able to have the ability to get into that cloned drive on my external if I need to add more stuff to the iMac or if I need it one day to boot up the machine. But I also want to be able to have Time Machine at hand to back up daily the little that is on my iMac right now. So I suppose I'm wondering how can I achieve this without the two conflicting or screwing up?