Yeah, my mod needs to be installed in sort of a strange way. There are a lot of files that need to go in different places, rather than fitting neatly into a sourcemod.

Inside the main file there's a file called README.TXT, which lists which folders should go where. Try using that, and if it doesn't work, post back here.

I know it's rather complicated, and the next release will include an installer.

If you read the readme.txt file that Felix told you to, you'll find this:
*
Hello, test subjects! To install the mod, copy everything but INSTANCES to [Steam]/steamapps/common/portal 2/portal2_dlc2*

So just select the folders 'materials' 'models' 'scripts' and 'puzzles' and copy them in that folder above, NOT common/portal 2/portal2/ or common/portal 2/. Then copy the folder 'instances' into portal 2/sdk_content/maps/