I've done this before. What you ned to do is re-create a directory for BVE routes in the OpenBVE folder(which is usually named openbve_stable when you download it). Just like in the C:\Program Files\BVE folder, you must make Railway and Train folders, with the Train folder housing all of the BVE trains and your Railway folder housing the Object, Route, and Sound folders. You'll have to do this manually, since most of the routes or trains use installers which install content to the default directory mentioned above.
On your flash drive:
-Place route object folders in the Object folder.
-Place route sound folders in the Sound folder.
-Place route...route folders in the Route folder.
If you can understand all of that lol
since OpenBVE is open source as long as the default directory for the BVE routes are made it will run them all the same way. I hope this helps.
BStyles