If you want to make maps that will work in Odamex, use the "Boom" configuration.
If you want to make CTF maps that will work in Odamex (and indeed in the other two source ports), use the "Boom" configuration until you are ready to plop down CTF starts and flags. Then, use the "Skulltag (Doom in Doom format)" configuration for placing flags and starts and only flags and starts, nothing else. Once you do so, immediatly switch back to "Boom" configuration. The flags and starts you just placed will show up as "?"'s instead of what they are supposed to, rest assured they will still work.
