Just use travel planner-better not that one linked on the pass, but f.e. bahn.de (=german railways) covers about all of EUR). The BEST choice is always the one for the country you are in-google is your best friend. IF you just fill in (name city) without any further, it will show all relevant stations. But most major cities only have 1 major station-most often called central.
Oh-in the distant past people did something very old-fashioned-they used guidebooks. Much of that is now also online. There were even dedicated guidebooks for specific train travellers.

BUT you have exactly found one major and very weak link_ THIS connection is not easy, dead slow, wants 2 or 3 changes en-route and has he need for cumbersome to make REServations inside Spain/on RENFE. The minor advantage is that you can hence use most major stops in Lisboa. And there is a very frequent-metro=subway lookalike line inside MADrid that also links all major stations (cercanias).