OS yosemite on SSD, applications on HDD - a little bit of chaos

I have a 2009 iMac 27" (11,1). It has a 1 tb hd inside and today I installed a SSD 120gb (using data doubler, replacing the dvd drive) from OWC. The install went well, no problems. I used a usb bootable and installed Yosemite on the "new" SSD. The plan was to use the SSD for the OS and the 1tb internal drive for all the apps, etc.
I made a new user account on the SSD, set it up to "point" to the home folder where all my applications are. I re-booted, everything was going ok, but then the hiccups started. I opened an CC 2014 InDesign file and half a dozen of the fonts were missing (even though they had been there a couple hours earlier). And in Google Chrome, some fonts on websites were defaulting to Times, and generally being annoying. Yosemite prompted me about a dozen times to enter my password to update the Library files... which seemed to work. Could it be a font problem?
I guess my question is, am I forgetting to do something? I assumed it would be a smooth transition, but there are kinks I didn't anticipate. Anyone with a similar experience?

Thanks - I hadn't considered that! Do you know the best way to uninstall and then re-install the Adobe apps? I have Creative Cloud subscription, so there's no issue with doing a fresh install.
If I'm re-installing Adobe, but still want to put the apps on the secondard drive (not the SSD where Yosemite is) do I have to do anything specific to update the Library folder on the boot drive? Or it will update files automatically? Thanks for your help!

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