A couple of questions though. Are you applying the staff style prior to entering notes or after? Applying the staff style prior should help with the layout issue (orange noteheads). Also, when setting up the instrument list, are you creating a new instrument for the bd/tam combo?
You could also use text expressions for instrument changes and percussion midi map changes rather than using layers. I'd even go so far as to suggest applying the staff style in layer 2 for the measures using the combo and using a text expression for a percussion midi map change prior to entering notes.
Let us know if you have any questions or need further help.