To Clone and use Time Machine

I’m running 10.6.8 and 10.9.2 on my iMac. My backup for 10.6.8 is close to being full and I want a second one to be on the safe side having one die on me a while back. I haven’t backed up 10.9.2 as yet. Can I clone both and then use Time Machine backups in the same partitions as the clones or should I have a separate partition for each clone and each Time Machine backup? My external will be a 1 TB LaCie and I’m sure there’ll be enough room for what I do.

Also, I saw some discussion about Time Machine in Mavericks not spinning down when using Firewire 800, so my 2nd question is if I eject my backup and then just disconnect it will it screw things up or would it be better to power down my hard drive before doing so?

Thanks,