Minimum yield strength should be the specified strength of your material.
Effective yield stress is used in CAN/CSA-S16 (Canadian Standards Association, Limit States Design of Steel Structures). For calculating the moment resistance of Class 4 sections the code offers an alternative method using what they call "effective yield stress". Here is an excerpt, "Alternatively, the moment resistance may be calculated using an effective yield stress determined from the width-to-thickness ratio meeting the Class 3 limit." This idea is also used for Class 4 sections in compression.
Unless you are using Class 4 sections and designing to Canadian standards you do not need to worry about this value.
In regards to your second question, I would like to offer some words of caution. I would be hesitant to simply design with FEA software with no idea of the process going on behind the user interface. That being said I will try to point you in the right direction.
Plates: used for loading out of plane, carry out of plane moments
Membranes: only support in plane forces and drilling moments
Shells: combination of plates & membranes, can also be used for layered and nonlinear analysis
Plates can be thin (neglects shear deformation, "Kirchhoff Plates") or thick (accounts for shear deformation)
It would go a long way to simply read the section on plates in the Advanced Reference Manual available under Help/Documentation/Manuals
Also, it would be worth your while to take a mechanics class in plate theory or a finite element analysis class that covers plates if you plan on using and relying on the output from SAP2000 for anything related to the safety of human life.
Great spirits have always encountered violent opposition from mediocre minds - Albert Einstein