As someone who regularly uses mvm.tf to make my MvM missions, it's a rather iffy website to use. For starters, I wouldn't really worry about the map that much, it only changes the spawnpoint names and nav_prefers, which is something you can edit in later.
When generating the popfile, it puts every robot into a squad (same deal on old.mvm.tf) and that's not really ideal. Only keep the robots that are supposed to be grouped together in a squad, you can remove the squad syntax for the rest. It also has the tendency to give too much info about stock classes (same on old.mvm.tf and even worse), you can safely remove the ClassIcon, Health and Name. Class and Skill are the only necessary ones. (Do this especially for stock Heavy and Demo classes since the icon mvm.tf gives for them are invalid)
Don't forget to name rename the popfile for your map, eg mvm_quetzal_b6_advanced(_name_of_your_mission).pop (The .pop is important)
Both websites are flawed since you're still required to manually edit the popfile afterwards, but I mainly use mvm.tf for its simplistic and organized mission overview.