Hi Rarebug, ok, without seeing your model, I'm still a little confused, but I think I can suggest a couple of things which may help you.
As you may already know, you assign a rigid diaphragm by selecting all the joints in a plane, then Assign Joint constraints, Diaphragm type constraint. Typically with a floor slab, you would use the Z default as the constraint axis, but in a vertical structure, use of the "Auto" feature would give you the same results.
It's your decision about this, but you have the option to model your slab using area elements (shell type with the properties of your slab). This takes more time to model, but it has the benefit of automatically providing you the slab self weight and and slab reactions for design of reinforcement. If you model/draw the slab, it will transfer shear and moment to beams, columns and other areas at shared joints, so you will need to draw it the way you want to transfer load, or use the Edit menu mesh areas to divide/mesh areas already drawn. CSI's ETABS program has better features for this sort of thing, but SAP can work well too if you know how to use the program
It's probably best to model your shear walls using Areas (shell type). There is a useful feature in SAP which can save you time here, it's called the 'Edge constraint'. After you've modeled the slab, beams, walls, etc. you can select objects, then go to the Assign menu, Area, and assign area Edge Constraints..these edge constraints automatically connect the wall to the slab, even when there are not shared joints.
You may have, for example, a more finely meshed slab and a course meshed wall. By selecting these areas and assigning edge constraints, you have saved yourself the time and trouble of having to mesh/divide the wall to share joints with the slab
Remember, in order to transfer loads betweens beams,walls, slabs, etc. there needs to be shared joints where load is transferred, or alternatively in the case of walls intersecting slabs, an Edge constraint
If this addresses your problem, try this modeling technique out on a small model first to get the hang of it