You'll have to pick a point at which to perform the modal analysis. For example, on a suspension bridge, you will want to perform the modal analysis after the dead load has been applied, which stiffens the structure. In the SAP2000 Analysis Case dialog box for the Modal analysis, select the...
It depends on what you want to do. STAAD is cheaper, and geared more towards buildings. SAP is a much better product for bridges, seismic, nonlinear.
I use both products. I disagree with fleisher, in that STAAD has given me more suspicious results, and crashed more often than SAP.
The big...