You can use all four parts together, but they are designed to be used independently as well. Each of the four parts is designed to be helpful in a very different way and not necessarily in a particular order.
The Base Set, the Featured Set, and the GrAASP are designed to be most helpful when all their measures are used at once, though there are many cases where a user may focus on a subset, for example when focusing on a single element of the Framework for Aligning Sectors. In contrast, given its length, the Compendium of Measures is intended to serve as a library of measurements, and you can select whichever seem most useful to you.