I'm using a sub folder within the /data/script/source/ directory to store and compile my scripts, I find it easier to manage my scripts that way, not to mention the convenience of bulk compiling.

The problem arises when using the CK to link my scripts to game objects. The CK kit is set to look for script sources inside /data/script/source/ but it doesn't look recursively, it ignores every folder inside. As a result it can't find my scripts.

Is there a way to force the CK to use additional script source folders?

As far as I know you cannot.

You can, however, force the CK to append a (up to) 4 character prefix to all auto-generic scripts via properties > scripts > prefix. If you add this same prefix to your handmade scripts, it makes it very easy to find all of your scripts quickly. This help for copying, deleting, bulk compiling, etc.

If you don't use prefixes yet, I strongly recommend doing so. Converting to the prefix system (Renaming) can be a pain though. .Took me ~12 hours to convert about 150 scripts over when I discovered the prefix system. (I use FSKR for Falskaar)

How did you do this? Did you just have to recompile them?

I haven't figured out how to rename scripts without making a duplicate with a new name. This has the woeful shortcoming of requiring all properties be refilled.

Autogenerated fragments have a "Rename" button in the other tab above them in the window. (Right above the dialog fragment there are two tabs, etc.) This goes for all 4 fragments. (Dialogue, quest, scene, and package)

For handmade ones you can rename the file AND the top line within the file declaring the name. Then just remove and re-add it to the objects it's attached to. You do have to refill properties, which can be a pain if they aren't set to auto.

Once you've renamed everything do a batch recompile based on your shiny new prefix and you're good to go. (errors will tell you where you've messed up and you can fix each case)

Like I said, this definitely takes a while, it's a lot of handwork, but it's definitely possible and worth it.