It was always important that those were installed in the correct order. As someone who first installed the Mojave Sub within a couple of weeks of its first introduction, I have had downloads of many updates along the way, not including the various paid add-on equipment packages (and a couple of free ones). Go to the "Run 8 Basics - Installation, Registration, Single-Player, Dispatcher Screen, and Multi-Player" page at their site at this URL:
#Download run 8 train simulator update
It looks like the process of installing the Needles Sub route and merging it with the Mojave Sub has been simplified somewhat, and is now handled through the update process. Not difficult, but just something you need to do. Bear with me while I recall the process and perhaps find some references for you. I'll get back to you further on this thread. There was a process for making this happen that I need to recall.
They solved the issue by making an intermediate Barstow-Yermo route, which is grafted out of the other two and acts as a kind of a bridge or keystone between the Mojave and Needles Subs. Initially when Run 8 came out with the Needles Sub, there were some issues with it working together smoothly with the Mojave. Once you have both the Mojave and Needles Subs, they must function together. Run 8 has many strengths, but good documentation is not among them. This is, regrettably, not well documented. The quick answer is that you must perform a merge process between the two routes, and then associate the various trains with them. I'll give you a quick answer for now while I look for further references to help you.