John you haven't given us enough information to give you helpful answers....by trying to decipher your posts I'm wondering if this is your question?
Do you want to install the Navs equipment into the TrainSimulations installation?
If the answer is yes then the installation path for the Navs equipment would be C:\TrainSimulations\Trains\Trainset --- or where ever you've installed your TrainSimulations routes....their installer usually points to a default place.
OR itself can have many profiles, each with it's own set of folders -- GLOBAL -- ROUTES -- SOUND -- TRAINS
The Open Rails program can be installed anywhere you want...it doesn't necessarily have to be in the windows program folders...you could install it to C:\ORTS\ORTS_Programs or just C:\ORTS_Programs
The manual has an excellent introductory section to OR and how to manage its' installation and profiles.