Why do I need to setup my MIDI Controller for each new song?

Am I doing something wrong? I am trying to learn how to enter notes effectively in Musescore and I am amazed at how good this program is.
However, I have noticed a weird behavior, where each time I create a new score, MuseScore forgets I had setup my MIDI controller and I have to start from scratch choosing my controller (which somehow appears twice, a version that works and one that doesn't. That's not MS fault, it's just a quirk of my keyboard).
Am I doing something wrong?

The other thing I wanted to mention, although it may need its own forum post and I am sure it has been covered, is that it looks like MS allows for only one single MIDI controller, instead of giving the ability to connect different controllers on different channels and/or use a secondary MIDI controller for note input and one for other purposes.

Practically speaking, besides my MIDI controller (which depending on which computer I am using could either be a cheap, slide-under-desk MIDI keyboard or a Yamaha Digital Grand) I also have what I would call a MIDI pad. It has "keys" of a sort but it's mostly for inputting drums or tasks other than actually playing.

Since it has fat keys, I was thinking of lowering the octave to a range I wasn't going to use and assign note lengths and other features through MIDI mapping (with clear labels) so that I don't have to use my mouse if I plan it right.
However, since I can only attach a single MIDI controller, and even at that I have to configure it for every new song, that's not going to work.

Are there any plans to make that system more flexible?

However, for the moment, I'd be happy not to have to set up my MIDI I/O for each new song.