Current I have used 483.11 GB of 1TB with approx 600 TB left over. I have 2x1TB External drives, and a 3TB, Could i tell which folders i want it to backup all i need is the main folders i use like Movie, Docs and Photos but if the computer goes errors i may have to restore back and i don't really want to spend a whole day installing all my apps again.
Yeah... that's going to be too much to fit on two partitions (one a clone and the other TM) on one disk. I would just use one of your 1TB disks for the clone and another for the TM backup. That would give you plenty of room for now.
I would not try to exclude anything from the backup to save space. Like you mentioned, that kind of defeats the purpose of being able to use the drive to restore from.