I have my own system of doing things as many do who use SP. The great thing is there are several ways to arrive at a look that works for you and those you draw for.
I personally like the foundation to be totally separate from the other parts of the model. But, I want anything that is part of the foundation construction to show in that plan and model when on it's own in 2D or 3D. So, I do like to have beams in the foundation plan and showing on the lower level plan. I try to keep it stacked just the way it would be built, and when placing dropped beams in the foundation below the floor system they typically sit in beam pockets. SP will not show a beam pocket if the beam is not on the same plan with the wall it is to pocket into. I also like to see where beams are in the lower level so I can map out walls, soffits, etc. It is crazy to do so much duplication, so often I will choose to place the actual beams where it makes most sense (foundation if pocketed), then represent beams on other plan sheets with a line and the copied notes if needed.
I also use an overlay plan for any floor I want to show an overlay of (master drawing I copy and paste my current floor plans into as needed). It has all the lines and layers preset to show how I want it faded and stacks well under my framing or other plans how I want. Tom Roman is the guru of master plans and having things set up for easy flow. Maybe he will chime in. Otherwise search for his comments on the forum.
Again, many ways to accomplish what look you are going for. Just got to explore and decide what works best for you and your clients.