The only way to "customize" the route is to define your own multiple segments. That is, if you want to go from point A to point Z, but also want to pass through points M and N, then you should download the route in segments: from point A to point M, from M to N, and from N to Z. Maemo Mapper will concatenate the segments together and guide you through all the segments in the order that you downloaded them, assuming you set the appropriate radio button in the "Download Route" dialog.

If you in-program UI is too cumbersome, you can go directly to the GPX Driving Directions web service that Maemo Mapper uses and generate the segments there. You still have to generate them segment-by-segment, though, but once you have the segments, you can open them in Maemo Mapper (in order) to get the same functionality as above.

The tap-and-hold menu's "Add Route Point" functionality is for defining your own route - it doesn't do any route calculation. Sorry it's not (at the moment) any more convenient than that.