bfillery,
I have tried adding them as "add frozen." This does allow you to use different cross sections. However, the issue of this is ANSYS Workbench does not connect the the bodies at the connection points. This is best seen by drawing two line bodies connected at a point and then running a modal analysis on the two line bodies. The mode shapes will show the two line bodies disconnected. This implies that the main issue is connecting two line bodies of different cross section. One would think a that "contact" or "spot weld" would be the answer but the ANSYS workbench help and tutorials never address contact between line bodies.
So the real question may be how do you connect two line bodies that have different cross sections?
-Jason Nicholson