Train from Berlin Bahnhof Zoo (or: Zoologischer Garten) leaves -38 and -04 from Platform 2. Same trains as from Hauptbahnhof; these stations are three (train-) minutes away from each other. RB and RE does not matter, for you it means the same. The RB train terminates at the airport. RB is a Regaion Train, RE is a Regional Express.

The routes are more or less the same when it comes to time. Central station is a tourst site itself, so it can be interesting to change there. Zoo is a tine station and the bus stop is just across the road from the station, so it is easier to navigate. But to be honest - even without the instructions you got here you would not get lost.

What means "late landing"? Until midnight nothing should be a problem. Berlin is a safe and easy place.

And Dresden to Munich? Train will take about six hours with a change in Nürnberg. Flight will be 60 minutes. Dresden Airport is 20 minutes out of town, easiest by taxi or train. Munich airport is 45 minutes out of town, easiest and cheapest by taxi. Don't thing about the american way of travel and avoid renting a car :-)