Here we go again. Sounds like you opened the route, gone to a session layer and added stuff. If so you are in the ROUTE and anything saved of the session depending on what it is will then pop up "overwrite route or save as new route."
If you had instead gone to the main (all) route menu, click on the route, then selected sessions (without opening the route) and worked on a session WITHOUT touching any layers, then on saving it will refer to sessions only and NEVER to the route (provided of-course you didn't do anything that is route related like add track). I highly recommend you do not fiddle with layers, because you seem to get lost in them, and unless you're very experience with them, there is absolutely no need for you to go near them. Like many of us say, KISS is the best way to go.
Remember, only ever open a route to edit it. To edit/make sessions open sessions (and not the route).