We will be staying in Meersburg and will be travelling to Baden Baden as our next stop on a trip through Germany. I had read that there is a Black Forest scenic train from Konstanz to Offenburg. It looks like Konstanz is a short ferry ride from Meersburg, so leaving from there should be no problem. However, when booking on the DB BAHN website, I get several different train options when searching from Konstanz to Offenburg or Konstanz to Baden Baden. My question is should I be looking at a particular train for the "Black Forest Scenic" train, or assuming they all travel roughly through the same geography does it really matter which train I take from the standpoint of having nice scenery along the two hour trip. Any help appreciated.

You don't have to go to Konstanz. The Black Forest part doesn't begin until after Donaueschingen. Just use "Meersburg(Bodensee)" as your start station and "Offenburg" as your destination and you'll be routed west along the northern shore of Bodensee - the first leg by bus and the next ones by train - through Ueberlingen, Radolfzell, and Singen along the proper route.

You'll be riding the normal trains through a scenic part of the country. But the normal trains going through the BF are the double-decker variety and offer nice views.

That said, you really should enjoy some time in the towns and villages along the way. Villingen, Hausach, Haslach, and especially Gengenbach are all wonderful, much more so than stuffy old Baden-Baden, IMO.

1. I would not go via Konstanz. The fast ferry does not take you to the city centre and train station but to the opposite side of the peninsula, so there is another bus ride involved. Unfortunately Meersburg is not too convenient for travel by public transport because it is about the only town on the lakeshore without train connections.
I'd take the bus to Überlingen, board a train there, and change trains in either Radolfzell or Singen. That should be faster.

2. All trains on that route will run along the Schwarzwaldbahn line (via Singen - Donaueschingen - Villingen - Triberg - Hausach - Offenburg, just to name a few of the stops). Look up train connections on www.bahn.de, open the "details" for the connections, and click the respective train's number and you'll see the entire route.

3. There is no need to book anything. This trip can be done cheaply on a Baden-Württemberg ticket if you stick with the hourly IRE or RE trains, and you'll have full flexibility during the day and also the buses included. Only the (very few per day) IC trains must be avoided with that ticket.

There is a bus from Meersburg Church to Konstanz railway station (via ferry).
The boats (not the car ferries) go to Konstanz railway station too.
Both solutions are usually more convenient than the Ueberlingen thing.

A little more complicated, but very scenic would go through Sigmaringen and the upper Danube river valley, all duapble on the Baden-Wurttemburg ticket