In order to customize one of the pre-configured GoTo systems, you will need to have the full version of MTpro with valid license. The license is required to use features such as ManModel and LayoutDesigner.
You can finde various downloads for each system on their respective page. The MTL file is an MTpro project that contains the BOM, 3D models, and other information pertinent to the project. Once you've opened the project, you will be able to add or subtract part numbers as you wish.
Once you have opened the desired system in MTpro, you can start adding (or removing) components from the system. To do this, you can search the product catalog in the left-hand navigation for the part you are looking for. If you want to ensure you are using only GoTo products in your system, download the GoTo Part Number List and make choices based off those materials.