So, you want to be able to select any type of PrBoom-compatible WAD file to run with DSDoom but just HATE having to constantly rename the WAD file to 'DOOM.WAD' all the time?
Simple trick....hex edit the DSDOOM.NDS file itself to auto-run that particular WAD file upon launch!
(NOTE: I use the OxED hex editor for OS X..don't ask me ANY Windows-specific questions...I'll just ignore you)
What you want to do is a string search for DOOM.WAD until you run across the string EXACTLY as shown in the attached image. Right behind that DOOM.WAD should be PRBOOM.WAD, if not then you're editing the wrong portion of the file.
Make sure you rename it to something else that also has four characters in the title, i.e. 'ULTI.WAD' for the Ultimate Doom WAD, PLUT.WAD for the Plutonium WAD, DOO2.WAD for Doom2, etc. Ensure that the WAD file you copy over to your flashcart is in the main root directory of your card and has the EXACT same name as your hex-edited filename.
Then just save the newly-hex-edited file as something OTHER than DSDoom.nds (you DO want original Doom, right?) and put that .NDS file anywhere you want on your flashcart. I keep mine in a folder called "_Homebrew". I've tested this trick with Doom2, Plutonium, and Ultimate Doom but it should also work with ANY 100% PrBoom compatible WAD file.
Post in here other WAD files you've gotten to work with it.
Again, this is just a simple hack until the DSDoom devs can finally code in a WAD selector.