the dosbox.cong is created individually for each game profile, and managed by using the expert settings. Which are basically the normal dosbox.cong txt file you know from the PC version.
It looks like you’re using the free version, so there’s only one profile. But you can e.g. setup the expert settings to your liking, and launch different games with different conf options from multiple .bat files. That’s how I do it on the PC, or did it in AnDosbox (like U7.bat, WC2.bat, settlers.bat, you get the meaning ?).