jchuzi,
I'm getting confused here, so let me get this clarified. Here's what I am setting up based on suggestions from TS people, as I upgrade from 10.6.8 to 10.10...
My existing EHD #1, 500 gb. It has 380 gb used so far with Carbon Copy Cloner which will soon clone 10.10 files.
New EHD #2, 3 Tb. Partitioned into...
Partition #1 - 1.5 gb for Time Machine
Partition #2 - 0.5 gb for cloning my current OSX10.6.8 so I can open my Freehand MX files in the future.
Xairbusdriver suggested a Partition #3 for cloning 10.10. Why? Doesn't my EHD#1 do that already?
So, do I need 2 or 3 partitions on my EHD #2?
Hope my explanation makes sense. Thanks!
Let me assume that I'm in your place and planning my next moves.
The internal hard drive has 10.6.8 installed, correct? When ready to install 10.10, I would make sure that the clone is up to date and then run the 10.10 installer on the internal drive. That will upgrade everything while keeping all your accounts, files, etc. intact. You will have an installation that looks like the old one except that it is using 10.10. (Programs that cannot run in 10.10 will still be there but they won't launch.) The external clone will remain untouched. If, heaven forbid, something goes wrong, you can always boot from the clone, erase the internal and start over.
To use your old system, you can keep the 10.6.8 clone
as is and boot from it when necessary.
Once you're up and running, I would maintain a TM backup of the 10.10 installation as well as a clone. I would also clone the 10.6.8 system regularly to another partition for this reason: If the drive that has 10.6.8 fails, you may not be able to recover it.
If any of my assumptions are false, or if anything isn't clear, post back.