Clean install of 10.9.2 on a separate drive: Home folder questions

Hi everyone
I've run 10.7.5 for a long time on an SSD in my Mac Pro with my home folder on an internal HDD.
Today I installed another SSD (actually a striped array of two SSDs on a Sonnet Tempo Pro) and put 10.9.2 on it.
Is it safe under 10.9.2 to use that old trick in Users & Groups -- right-click the user name, select Advanced and choose the HDD as home folder?
Also, I've seen comments that one shouldn't have the entire home folder on a separate drive if that drive is a mechanical drive. Can someone point me to instrux on which parts belong best on an SSD and which on an HDD and how I go about selecting them?
Many TIA
Philip

Hi. Thanks for the reply. Does Time Machine by default exclude System and Applications Folder (I didn't click any option to exclude those I remembered)? How do I not exclude the Applications folder and System files this time around?
In Time-Travel view when I point it to the Applications folder, it switches to the Volumes folder and the Restore is dimmed. I wonder if it's incompatible because it's not Apple's Time Machine or it's a bug with Moutain Lion (the drive is backing up the new clean install of Mountain Lion now but when I test it, use Migration Assistant if I need to restore things again, it still doesn't see it as a Time Machine backup).
What could be the solution? Should I reinstall my applications again (I guess that's a blessing in disguise, now I can declutter)?
Thank you.

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