Are you running SE4 Gold 1.91? Specifically, a Version of B5 Mod that has been made playable in Gold?
The instructions are still helpful in that they tell you which files are modified by FQM. You have to merge them into the mod you are combining FQM with... TDM is just a special case in that it doesn't modify the data files (other than Formations.txt). As stated previously, you will lose the customized changes to quadrants in B5 Mod, such as Hyperspace systems, by just putting the FQM files in there. If you do not mind losing these, that will partially suffice. You will still need the population modifier settings from FQM, located in Settings.txt.
These two files should be used as well. They contain many more formations and strategies than are in B5 Mod, as well as being designed to allow up to 101 ships to work in a formation, rather than the 27 or so that the limited files in B5 Mod allow (as they were designed for SE4 Classic (1.49), which did not allow up to 101 ships in a formation):
DefaultStrategies.txt
Formations.txt
Note that Formations.txt is the file containing formation information for fleets. DefaultStrategies.txt provides many customized fleet strategies for the player to use. These are from
Ultimate Strategies Mod.