Hi Steve,
Apart from defining whether a fill is 'Core', 'Finish' or 'Other' in the profile manager, there is no other way of controlling the visibility of the individual parts in a complex profile at the moment.
Never-the-less, there are several advantages of separating out each element into its own individual profile and assigning each to a different layer; it gives you the opportunity to fine-tune the 2d display of the elements individually; doors & windows tend to 'play' better in a simpler wall (the GDL gets confused as to what is the face of the wall!); and it will actually reduce the number of unique profiles needed to deal with those awkward special situations.
Personally, I don't think having layers in profiles would actually make life any easier so I wouldn't recommend it, but you are very welcome to create a wish in the 'Construction Wishes' section of the forum to gauge other peoples opinions.