Jacek
That's gonna be fun...
I would suggest (although I have never done it myself, Door and Window builder has always got me thru, but isn't going to do this one) you will have to create custom windows, modelling all the elements in plan, using slabs i believe for frame, mullions, glass etc, then have a slab which is the overall shape of the window, with an ID of WALLHOLE. Check out custom windows in the Help menu.
For the parapet, I would again model this on plan with a slab the shape of your elevation (maybe just from your dotted line upwards?) then view from what will be the top, in 3D window and save as an object. You can then place that object in plan at the correct elevation, and if the material on the face of this, and on the face of the wall are the same, there should be no line between the two. Again, this is probably better explained in the Help menu.
As far as redesign goes, I would probably have two walls on existing and new layers, each with appropriate windows / openings depending on how you intend to change them.
Good luck.