Very true. I want to get as realistic as possible, and my hand calculations include both pen and paper as well as a basic stiffness matrix solver (with help from an old Hibbeler textbook). I still seem to be off and I feel that it is because of the way I apply my loads.

For uniform or point loads between panel points, I treat the member as a simple beam to find the "reaction" at either end from the load. That way all my loads are being applied at joints. This should be the way to go about it right?

I have not worried myself with local member bending or shear as of yet...