In ver8.4 you can control this using load groups (see FEAP User Manual) in the specification of the boundary conditions. This allows you to specify which proportional load is to be applied to the various parts. If it is from an element body force loading the same thing can be done using the GROU material command option, which also requires specific proportional loads.
Older versions are more difficult to control. You can use FPRO mesh commands to associate specific proportional loads to forces and displacements.