The final bit of the config file you should definitely change is in the autoexec section. This is where the AUTOEXEC.BAT batch code is recorded. This code runs every time you start up DOSBox.
Breakpoints at other locations should work fine. With a 32-bit IDA, you will have to build a 32-bit dosbox, even on 64-bit platforms.
libretro wrapper for DOSBox * To use you can either load an exe/com/bat file or a *.conf file. * If loading exe/com/bat the system directory will be searched for a 'dosbox.conf' file to load. If one ...