After testing mmapper2 some time and talking with Caligor I feel I need to give a few hints on how to map certain areas.

The best results I got in most areas were achieved by just running around xp-ing or pk-ing and not caring for the mapper. It will create a bunch of rooms via automapping and you will be able to recognize the areas afterwards. In some places you will have to shift the rooms around a bit. This is especially the case where rooms of different scale factors meet. For example Bree's surroundings will look strange if you started mapping inside of Bree and then went outside. When following this strategy you don't need to care about the mapping parameters. It works quite well with default parameters. And generally don't worry if mmapper creates lots of temporary rooms. In some places it's hard to decide which path is the best one and that's why it keeps a few guesses around for some time. Eventually - especially when you enter previously mapped terrain - it will decide which path was the most likely one and accept that.

Unfortunately there are some places where that strategy doesn't work well:

1. Areas with lots of rooms that look exactly the same, for example the area around northern Greenway. The problem here will be that mmapper maps many MUME rooms into a single room on your map. There are two ways to cure that. Either you can align the correct rooms as they should be and delete the wrong rooms after mapping, then go there again and purposely visit the "holes" in the map you created. If there is some "skeleton" of correct rooms the others will be mapped correctly, too. This involves knowing which rooms are actually correctly mapped and where they belong. 
The second possibility is temporarily setting the "correct position bonus" configuration item to something high - for example 50. Then you can slowly walk around in the place you want to map and it will create a new room for every step, if there isn't already a matching room in the expected position on the map. On the one hand this only works if the area is "geographically correct", meaning that most exits connect rooms directly next to each other on the map. On the other hand this strategy also works if you have no idea how the area looks like.

2. Areas with lots of random exits and lots of rooms that look the same, for example old forest. Here mmapper will fail horribly if you don't assist it manually. It will create a few rooms that are strangely connected and it will probably find out when you leave the random area again (if not, press the "stop" button in the tool bar). That's all you can expect there. The map it creates will certainly not look like you imagine the area. Here only the old fashioned "coin method" helps. Drop coins in certain rooms and map the area in your mind first. Then create new rooms and connections manually according to what you think it looks like. If you walk along the manually created exits afterwards it will update the manually created rooms instead of creating new ones.