Installing OS/user folder on one drive, apps on another

I have two Velociraptor drive that are RAID striped as my startup disk. It's caused some some problems. (like Boot Camp won't work on RAIDs, Each drive shows up separately when Option key booting, etc)
So I'm thinking of splitting them up into two normal drives. But at 300GB each, they aren't big enough to store all my big apps, the OS and my huge user folder.
I heard there's some problems keeping/linking your user folder to a non-startup drive.
But is it possible to install apps on a non-startup drive? Do they all expect to be on the startup drive? Do I need to remap the HD/Applications folder? Many apps (esp. Adobe's) install lots of files in HD/Library/Application Support. Is that going to confuse things?
Love to hear some tips/warnings/suggestions.

But is it possible to install apps on a non-startup drive? Do they all expect to be on the startup drive? Do I need to remap the HD/Applications folder? Many apps (esp. Adobe's) install lots of files in HD/Library/Application Support. Is that going to confuse things?
There are basically two kinds of program installation methods for the Mac - those that are dragged and those that use an installer. Any program that is installed by dragging can safely be placed on a secondary drive. Those that use an installer are a bit more iffy. Some installers let you specify the installation location and these too can safely be placed on a secondary drive.
Those that automatically install in the Application folder of the boot drive - I'd hesitate to move them. The problem isn't that they won't run properly; what I'm concerned about is updates. If a programmer/vender expects the program to be placed in the boot drive Applications folder then its updater will probably expect it to be there too and the update will fail. To reduce confusion I'd keep these programs on the drive where they were installed and make an alias of them to the secondary drive.

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