Using Mapster32 to create content and EDuke32 to play it doesn't mean you can't make it compatible with the original DOS version of the game. In fact, Mapster32 has some clever map-corruption prevention in which is completely missing in the original build.exe, so it's way less likely for you to break your maps (in fact, if you open a lot of old maps, even the ones in the original game, you see a lot of corruptions that might break those maps in the long run if you were to edit them further). The interface is much more user friendly and faster to use, so creating new maps is a whole lot of faster on Mapster32.
EDuke32 reads regular CON code fine so there's really no reason not to use it. As long as you're not using any EDuke or EDuke32 specific commands, the same code will work in all (1.5) versions of Duke3D regardless.
There is no real modern guides for 1.3D/1.5 CON scripting around, but this is a good place to start. Feel free to create a classic CON questions thread on the forum as well if you have any questions.
There's already a mapping questions thread for any mapping questions you might have.
