I don't think you should use in-place families to be hosts for doors or windows. If the Revit is so categorized, just leave it be... Whenever you try doing something that programmers didn't predict, you end up with unexpected results.
The way you could have create those walls is by using multiple wall types. I assume that this is some masonry. You can solve this just by using two or three wall types which are in some hierarchy (major, minor, etc...). Use one major wall type everywhere. Then, the spots where you have thicker facade can be created with minor walls which have just one layer (facade material), but are joined with this major wall which may have multiple layers. Even if major wall has multiple layers (which I assume that it should), its facade material will join with material of this one layered wall that you used to play with the facade.
I think you spent a lot of time making this in-place family, am I right? The way you model is more appropriate for Maya or 3Ds Max....I don't think that in-place families are men't for creating walls. Revit uses system families for this. Use in-place families just for some non-standard details etc.... That is their purpose.
Since you re in this mess now, try using curtain walls instead of windows and doors. Curtain Walls have a large opening which cuts like knife through butter. Maybe it will save your work, so that you don't have to model all over again.....
Andrej Ilić
phonetical: ændreɪ ilich
MSc Arch
Autodesk Expert Elite Alumni