i'm modeling a manipulator too, using SimMechanics. I'm encountering some problems as well and still can't solve it. But I thnk I can giv you some suggestion

maybe you can try this:- draw your robotic arm in SolidWorks software, then use SolidWorks-to-SimMechanics translator to convert your drawing into Matlab-Simulink's blocks. Then open your matlab, build the blocks by using SimMechanics toolbox. The simulation will appear as like your SolidWorks drawings and you can determine its movement

you might need to adjust and put some actuator+sensor into it, dependng on your robot design

you need to have: Matlab (I recommend 2009a and above), SolidWorks-to-SimMechanics Link (download it from internet), SolidWorks software