The whole point of creating BIM models is to reap as much benefit from them as possible. One benefit for structural engineers is that when you create a physical model, you can create an analytical model simultaneously, saving you time later because you can send it straight to structural analysis software instead of creating it from scratch.
So, with that in mind, here is one tip about analytical lines for beams.
If you want to have a physical beam under another beam but keep the analytical lines at the same level, then use the z-offset in the beam properties instead of moving the beam down.
Analytical and physical model goes into the same location: