Hi Joe,
The tool library is stored inside the config file - but you can run PixelCNC on whatever system that has it and then go File->Export Tool Library to output it to a file that you can move between systems. Then you run PixelCNC on the system you want to use the tool library on and go File->Import Tool Library, which will copy the tool library into that system's PixelCNC config. The import/export tool library functionality is just for externally backing up or transferring tool libraries between systems, it's not something that PixelCNC will continue to reference for tool definitions.
Thanks for the question. Hope that helps!
- Charlie