Chris,
What is the purpose or goal of your analysis?
Is it stress? deflection? or is it modal?
If it's stress concentration at the joints, you may have to do the analysis in two steps:
1) A complete assembly in order to find the areas of the model with higher stresses
2) Then model a 'cut out' of the region of the previous model with the objective of predicting more accurately the max stress.
For step # 1 you may use the flat surfaces as you're currently doing. (Have you tried rigid links? I can give you additional details to use them correctly if you like).
For the second step you may have to model the weldments or bolts in a more detailed way.
On the other hand, if the goal of your model is modal analysis; what you're currently doing might be just fine, because modes and natural frequencues are global properties, less dependent of the way you connect the components. Not that you don't have to model the connection correctly but that small deviations from the ideal model have a lesser effect on the results beacuse the objective is to determine a global and not a localized property or result, such as stress or deflection.
As for the person whowrote that Pro-mechanica only joins the elements at the nodes for two touching surfaces, that is not correct. The two adjacent volumes become as welded as you can get it at the common surface;one advantage is that you can give different material properties to the two touching volumes, if that happens to be the case. Of course, since the purpose is to model as close to the real object, then modeling as bolts or weldscan bemore appropiate.
I hope all this rambling helps.
Sincerely,
ghgarzon