As the travel is in Germany, I would go to the German rail planner Bahn.de, which has the option to select 'all stations' for cities. (It is available in many languages, I have selected the English version here.)
When you enter the name of a city the site knows has several stations, it gives the name in all capital letters as well as in normal capitalization with the names of the different stations.
Run the search with the city name in capital letters and you will get all efficient travels in the results, each with the station used for the travel.
If you select one station in your departing city, you will still get results, some of which may have the trains you are looking for, but maybe not all of them. And if you selected the 'wrong' station you will often get a short hop to a near station and a change trains.
While traveling within Germany, this planner allows you to state your actual departure address (home or hotel for instance) and your actual arrival address, and it will tell you which local transport to the station you can use and so on. In which case it will always go for the one best suited for your long distance travel. (But it may still take a short hop to an out of town station if that happens to be a shorter overall trip.)
If you use a rail (or general travel) planner which does not allow for an 'all stations' option, just select one station at random, run the search and repeat with a different station till you get a clear picture which station is the best for your journey.
For your city pair of Berlin and Leipzig, both cities get the Hauptbahnhof indicated. With for Berlin the addition of 'tief'.
Click on Details for this journey and you get more information.
If that is not enough for your (it might not be for me) you can either use the map option, zoom in till you get the details for the station you want to know more about, or use the option of more details for the stations, which includes the full address of the stations, one at a time.
If you want to start from a different than the indicated station or want to get off at a different one, you can, again in the details, get 'Show intermediate stops' and see which alternative stops this one train stops.
I do not see it on this site but many rail planners show 'all trains from this station'. Which will help you with alternative times for the same route.