CCC and Time Machine are two completely different solutions.
Time Machine makes automatic, scheduled backups of any changed files (so each 'backup' consumes about as much space as the data that's changed since the last backup).
CCC clones an entire drive, so each backup consumes as much space as your entire disk, regardless of how much data has changed.
There are pros and cons to each approach. With CCC you could essentially reboot your entire system to the point-in-time the backup was taken. However, you need far more disk space to do so (at least if you want to keep more than a handful of snapshots.
With Time Machine you can restore individual files from any snapshot going back as far as Time Machine has history for, but you need a working OS to restore to (so it's not as handy if your entire OS drive fails)
Is there anyway to specify which drives or which files on which drive TM backs up on
Sure. The Time Machine preferences lets you choose which disk to backup to.
TM is currently telling me there's not enough space on my Terabyte drive and rather than delete how far the backup go I can only stop backing up Library and Apps folders, which are pretty crucial.
How big is your Time Machine drive? How big is your source drive, and how far back do your TM backups go?
Personally I have over a year of TM backups on a 1TB drive (with plenty of space for more). Of course, each person's backup will be different depending on the rate of change of files on their system, but your post implies that you don't have a long Time Machine history (unless I'm mis-reading your post).
Should I just use CCC for everything and TM is not actually backing up my backup from CCC.
Use whatever you like and are most comfortable with. For some people, TM is the best thing since sliced bread. For others CCC is the right option. For others, neither option fits their needs.