JB,
I do exactly what you're after as standard practice. Here's how:
No separate story for the floor system. Rather, the floor sheathing (normally plywood) is done with slabs or roofs (for decks) on the floor it 'belongs' to, i.e., the second floor's floor sheathing goes on the second story. It's beams and joists go on the story below.
This way, for a framing plan, you have the sheathing set up to show one-story-down, which makes it appear as a dashed outline contour on the floor below. You lay in the beams and joists on the floor below using the beam tool for simple homogenous or rectangular sections and objects for W shapes, TS's, etc.
Also, I have separate layers (and their names in parentheses) for the following:
-Sheathing (3D-FRAM-FLOR-SHTG)
-Concrete topping (3D-FRAM-FLOR-CONC)
-Major homogenous beams (3D-FRAM-FLOR-BEAM)
-Steel beams (3D-FRAM-FLOR-BEAM-STEL)
-Concrete beams (3D-FRAM-FLOR-BEAM-CONC)
-Joists (3D-FRAM-FLOR-JSTS)
I have a analogous layers for roof framing, that start with "3D-FRAM-ROOF-**
I also keep wooden and steel posts on separate layers. When I need to provide steel drawings to fabricators, I can reduce views down to just the steel elements, and view them at will using section / elevation views.
This system allows you to do your framing plans 100% parametric with no cheating and no 2D edits.
Another tip: For the standard beams and joists, have them display with a halftone (or invisible-in-layout mode) pen for their outlines, or even a dotted linetype, and the centerlines with the lineweight / type you'd normally see for a framing line drawing. You can also set up a display option pre-set to make the beam elements show 'centerline only'.
Works like a charm. I wrestled with this over many projects in my early days using AC, and this is where I settled at. With the exception of studs, I usually model every stick in the building, too... No guesswork, particularly when routing drain piping, ductwork, etc.
The only time I introduce an auxiliary story is if I have a truly separate and complex ceiling arrangement... like you'd see in one of Wright's Usonian homes. Even at Taliesen, in the old days, Jack Howe would have the 'boys' (of which quite a few were ladies!) draw a separate plan for the 'deck' (really soffit) framing.
BTW... It's worth seeing some of the drawings those folks produced back in the day... They were truly beautiful. You can also see the hand of other hit makers in some of them. Richard Neutra's hand is obvious in the landscape of some the renderings produced in the mid 20's.
Congratulations for going 'hard core'... That's how you'll harness the real power of this software, which is truly amazing.
Happy framing!