To label the manuals and pedals separately, for the time being I suggest you create the ‘Organ (2 staves)’ instrument, then add a single-staff instrument below it and edit its name to be ‘Pedals’.
You can choose whether or not rests of identical value in opposing voices should be shown as a single rest on the Rests page of Notation Options: look at the ‘Rest positioning’ section.
And to reverse the order of accidentals, select the notehead in question and in Engrave mode, edit the ‘Accidental column’ property (not the ‘Voice column index’ property).