Analytical model lines

[Galadriel]

I was wondering if someone can clarify the following question.
where should the location of the analytical model line should be.
I have a floor elevation set at 12'-0". The top of my beams is at -8 1/4" and the top of my joists are at -5 3/4". I have changed the elevations in the property elements by changing the start and end level offsets. when I do this i don't get the "gap' between the beam and joist. what I ended up doing was right clicking on my beam/joist and clicking "detach from plane" then went to the element properties window and changing my "z-Direction Justification" to "OTHER" and then changing the "z-Direction Offset Value" to the elevation that I want my beam/joist at. By doing this I keep the analytical model line on top of the beam/joist. when I copied the floor slab from the architect and changed it to structural in the slab "element properties" window. when I went to the 3D view and noticed that all my analytical model lines were moved to the floor elevation (12'-0"). shouldn't the analytical model lines stay on the top of the beam/joist?
I hope the above makes sense and some one can clarify it for me. Thank you.

[efink]

What analysis package are you using? We use RAM Structural System and have run into problems if you offset beam from the top of slab elevation. During import some of the beam ends have returned to the 0" offset. To combat this we have been creating a top of steel level and offseting the up joists from that. In the girder and joist element properties we change the Auto-Detect Vertical Projection to the top of steel level. Overall, removing the Auto-Detect Vertical Projection from all framing and column elements appears to the best way to control how the analytical lines connect. When using the links for RISA and RAM, export by selected items only to keep to top of slab levels from being included in your structural analysis model.