It's really quite a complicated procedure, I'm afraid. Firstly you need to use the tool to capture the textures from the level files on the CDs. You want to capture the UB level that you are intending to work on, and all the TR levels. The tool will capture the textures in a special folder structure that Glidos understands. For each level there will be several folders with 32-digit hex names, and within each of those several images with names made up of coordinates. What you are trying to construct is a file (known as an equiv file) that will tell Glidos where the UB level images can be found within the TR levels.
Once you've captured the UB level you wish to work on, and all the TR levels, make a copy of the UB level folder. Call it LeftToDo (say). Then make another copy called Working (say). Choose a TR level and copy its 32-hex-digit folders into Working with the ones from the UB level. Now you can use the "Generate" tab on the tool to create an equiv file from the "Working" folder. Inspect the equiv file to see if it has any mapping in it (it's just a text file). If it has no mappings, you need to try other TR levels until you find matches (each time deleting "Working" and recreating it from the UB level and the new TR level). Once you have an equiv file with mappings, keep it safe. Perhaps put it in the TR level folder from which the mappings came, or give it a special name to denote which TR level it came from.
Now look at the mappings in the equiv file. One part of each mapping will be the path of one of the image files in "LeftToDo". For each one you find, delete the image from "LeftToDo". This is important to avoid conflicting mappings. Now repeat the process for each TR level, keeping each equiv file safe.
Ok. That's most of the work done. Next you should collect all of the equiv files into one big one. Use cat on unix or drop one after the other into a text editor. DON'T then delete the individual ones. They might be needed if something goes wrong later.
Now you need to update the texture pack. Shouldn't matter which texture pack you choose, other than it needs to have textured the levels of TR from which you found mappings. You'll find that the texture pack already has an equiv file. You need to join your equiv file with that of the texture pack, and then replace the old one in the texture pack with the the result of the join. You CANNOT use unix cat or a text editor this time. You must use the "Join" tab on the tool. That will take two equiv files and generate the join.
That's it. Good luck.