New instruments

You can customize the instruments.xml file - see Edit->Preferences->General to see its location on your system. You can either edit it in place or create your own customized copy and then tell MuseScore (using this same dialog) to use your version. The syntax is not terribly difficult to figure out; just load the existing instruments.xml into any text editor and search for various instrument names. You can either change the existing Baritone to use bass clef and transpose accordingly (just steal the tenor saxophone settings) or create your own instrument, perhaps called Baritone (TC). Note that while marching bands and so forth do use treble clef (and transposed) baritone parts, apparently orchestras do not do not - baritones read bass clef in concert key. So it's probably worth having both instruments available. Similarly, you can add Eb tuba by copying clef and transposition settings from baritone saxophone. Just use the correct MIDI settings so playback uses the right instrument.