If I were you, I would do an assembly and save the assembly as a part for FEM. This way, you will have one entity with preserved beam information (This should also work if you save in any neutral file format).
Hope that helps
using SolidWorks "weldments" feature, you can have as many structural members in a single part as you want. I have weldments with hundreds of various beams and tubes and plates and angles etc, all in a single part.
AND Simulation loves it!
I found a solution, just put the two parts into an assembly, and be sure that they touch then joints are good.