I am having a similar problem. Using ADA 2008. I'm giving myself a crash course and designing my own house to build. I've sucsessfully designed the first floor and added a Dutch Gambrel roof. I'm stuck at extending the outer walls up to the roof and drawing my layout for the second floor. (Everything goes to the first floor) Still trying to decipher Project Navigator and Xrefs.... But as stated above, I'm a one man show and trying to do this all in one drawing.
I'm also learning ACA 2010 on my own, and both books I'm using are very good for learning how to create levels. The books are Accessing AutoCAD Architecure 2010 by William Wyatt, and Mastering AutoCAD Architecure 2010 by Paul Aubin. Wyatt's Stairs chapter is when it all began to really make sense for me.
Others may have a better/ different answer than mine but here is how I would tackle your problem.
The walls that extend up to the 2nd floor from the first floor should be in a separate construct from those that exsist only on the 1st or 2nd floors. This construct should be tagged as "Spanning" both these by tagging both levels on the construct properties in PN. Then when you create your view drawing ACA will pull it in to both your first and second floor drawings.
The walls themselves should then be drawn to their 'true' story-spanning height, instead of as multiple pieces at the first and second floor heights.
One thing that's helped me work my way through these sort of problems is to remember you're putting the model together in the same fashion as the house is being built. If you need a beam pocket in a FDN wall.. you're really carving that space out of the form. That's a body modifier in ACA. The same with these spanning constructs.
That's just my .02 as someone who's only delved into ACA extensivly for the last 7 months. I'm probably missing something important there with regards to cut planes and visibility states. Hopefuly I've given some direction for you to investigate.