Hi Joe,
The tool slot numbers in a project are what is used as the tool index in exported G-code. The Tool Library is only for storing definitions that can be re-used in a project, by copying one or more definitions from the library to a project. Changing a tool definition in the library does not change that tool definition for all projects that have previously copied that tool definition to themselves - it is just a list of definitions that a project can copy from to its own tool definitions so that users do not have to re-define the same tools for projects.
Two different systems running PixelCNC could have different tool libraries, which is why exported G-code uses the tool slot number in a project rather than the tool definition index from the library. You can organize your tool library to reflect the tools you have setup in your tool changer, for up to ten tools, and then use the Load Library To List button in the Project Tools mode to automatically copy the first ten tool definitions from the library to a project. It is important to remember that this is only copying whatever definitions currently exist to the project, and is not storing references to the tool library's definitions in the project. Otherwise opening the project on a different system with a different tool library would not end up with the same tool definitions for the project.
Hope that helps. Cheers! :]
- Charlie