I have similar concerns so what I am thinking of doing is to create in the roms folders a pc-gamedata sub-folder where I would place the game data. In the pc folder, I would only include shell scripts. For example, to run Dangerous Dave, the script would be:
#!/bin/bash
/opt/retropie/emulators/dosbox/bin/dosbox -c "mount c /home/pi/RetroPie/roms/pc-gamedata" -c "c:" -c "cd DDAVE" -c "DAVE.EXE" -c "exit"
DOSBox should be configured to run scripts from EmulationStation. If not, then update the RetroPie setup script and run the following command:
sudo ./retropie_packages.sh dosbox configure
I appreciate it’s a lot of work creating scripts, especially if you have a lot of games but it will give a neater appearance in ES.
For more info, please check at my tutorial at link below:
http://dosonthepi.blogspot.co.uk/2015/01/run-dos-games-in-retropie_15.html