You are correct and so is he, though there may be some drawbacks to his idea.
To use 2 batteries for a 12 volt motor the batteries are connected in parallel and both can supply current to the 12 volt motor. That is to say that the positive of both batteries are connected together and to the positive lead of the trolling motor while both negative battery terminals and the negative lead on the trolling motor are connected together. The advantage here for the 12 volt motor is that you have two batteries worth of capacity supplying you motor. This is called a parallel connection.
To use 2 batteries to power a 24 volt trolling motor the positive lead from the motor is connected to the positive terminal of battery number 1. The negative terminal of battery number 1 is connected to the positive terminal of battery number 2 and the negative terminal of battery number 2 is connected to the negative terminal of the trolling motor. This is known as a series connection and provides the voltage of the two batteries added together (24 volts). The advantage of this setup is that it takes less current for the same amount of power output. Other 12 volt loads can be hooked up to either battery but remove energy from just that battery and the 24 volt string is only as good as the weakest battery as the 24 volt load requires the same amount of current be supplied by both batteries.
This brings us to your buddies situation. Hooking up the batteries in series will give the 24 volt setup and the 12 volt motor can be hooked to just one of those batteries. This will work fine until he uses the 12 volt motor for a while and then wants to switch to the 24 volt motor. He may find that he has removed enough energy from one of the battteries that the voltage collapses and the 24 volt motor will not run very long or at very high levels.
If space and $$$ allow I’d keep the batteries seperate or better yet change everything to 24 volt.
Hope this helps. If you have other questions just follow up here!