How do I make train reservations?

For Germany, don't use a rail planning app or Eurail, definitely not rail Europe. You can get reservations for trains in Germany from the German Rail website. There is a link at the bottom of the page for "Seat only (no ticket)".

In Germany, only long-distance trains (ICE/EC/IC) even have reservable seats, and most of the time reserving is not necessary. In about 150 days (over 15 years) of traveling in Germany, I have only once been on one of these train where all of the seats were occupied, and even then, most were not reserved. You can always reserve a seat at the ticket counter just before boarding.

"We have Eurail Select passes..."

First class passes normally mean you sit with fewer other passengers in the first place. You'll likely have a good choice of seats without reservations. Holidays are the exception but I don't think there are any in September. I've traveled often in Germany over 4 decades in 2nd class and never really needed reservations. I don't think you'll have a problem.

I've been on maybe two ICE (fast trains) where seats weren't available and we had to stand in the vestibule, both times were in the summer and on popular routes that didn't originate from the station we boarded at. I rarely bother to make reservations.

If you do want to make reservations, you can do so with your smartphone/tablet via the Deutschebahn app, or just in person at the ticket machines or at the DB travel center (but there will be a wait, so you might as well use the machines).

I have much less experience on German trains than the other posters above. However, when going from Berlin to Dresden and back in 2012, someone on this Forum recommended my mother and I get reservations, and I was very glad we did. Particularly on the way back, the train was quite full, it was the old compartment style, and people were sitting on their luggage in the aisles. But with reservations, we just went right to our seats, stowed our luggage above them, and settled in. Well worth the small extra charge (€4 at the time, a bit higher now). So, if you're going on a busy route at a busy time, do consider them.

If you purchased a two-country pass, then you may have chosen the 2nd-class version. But I don't think that makes much difference in the rest of the advice above. You need to have the pass activated at the first train station, so if you want to make an optional seat reservation or two at the same stop, then that's another opportunity. I'm not aware of any daytime train that currently requires reservations within these two countries (but overnight and to other countries do).