If you clone your system - and hope you have looked at and used / tested CCC already, nice to do a walk thru and test it all out and get the feel for it once -
you clone the system then you have cloned Applications.
What you also want to do is include JUST the minimum from /Users/my-account/
- such as ~/Library and maybe Documents but small and nothing else.
You want to copy your user folders such as Documents... on to the end, and anything else, to another drive ... ideally.
Now have a clone of the old sysem
Have copied all the important media files, folders, documents to another drive
Have an installer for OS X ready
Installed clean system to SSD
Setup Assistant will ask to import to Mac OS X on the SSD from your other system that you want to import, and you only want to import your apps that you trust are compatible and current. Those that have installers sometimes best to use the installer. Your prefs and mail are in ~/Library. You want that.
The user home Library gets a lot of hits on IO for reads and writes and best to have on the SSD - rather than have on another drive. If you want the entire user account on another drive, as one or more tutorials show and which is easy to do with Accounts settings in OS X, go ahead. I don't, I left mine on the SSD.
I would clone your SSD soon after you have it the way you want it.
And after all the disk I/O and writes, even with TRIM, I would boot from a system running Mavericks and run DU Disk Repair (never run DU from an older system on a newer OS).
Fantom drive - these are green? and uses USB3? something else? connected to a PCIe card? and 100% worthy of trust, right?
And you are going to use one drive, partitioned, with partitions for cloning the system, small 200GB, TimeMachine, 350% capacity of what you would ever need, and maybe even a data clone partition? Fine. Ideal is to have two drives, two sets, not have all your files and backups on one drive if the drive fails for some reason. Convenient as it is.