I've got MuseScore here, although not the latest version, so I don't know if there are any extra options in that.
MS will read in the note info from your midi file, and will act on that. The assignment of the pp/ff etc marking is literally as per the midi input. However, within MS you can edit this info, note by note, or by block, as you see fit.
You can handle this in any way you like, to achieve the effect that you want. That's what is important. But remember, anyone later performing your piece, or your arrangement, may well 'interpret' your instructions as per levels as they see fit, to get the effect that they want. That's what performers (conductors/musicians) do. Like it or not.
If you play a piece of music and record the midi, then the velocity levels will probably be all over the place. That is normal. The piece has been totally 'humanised'. If you then adjust the velocities to get then looking 'regular', then you may find that the playback is much less 'humanised', even becoming robotic, and the result may not be any use. You may need a compromise.
If you can get a midi recording made by a good musician, there may well be less variation in the velocities. You need to study the variations, and note how the patterns of the variations of the velocities relates to the structure of the music, the bars/phrases etc, and consider why that is. Why the performer has chosen to do it that way. I'm sure it's not accidental. If you wish to change the velocities, then OK, you can do so, just like a different performer might do, but you should have a musical reason for doing so.
Does this help you any?
Geoff