Both of the options you mention are possible:
> Allow a dwell period in the beginning so the model can reach equilibrium before I send it motion commands
Sure - just delay any changes to the inputs to your model until enough time has passed that the transients settle out.
> Or could I make the dwell a separate simulation and carry the states over to the next simulation?
This also works. You can save a Simscape Operating Point to set the initial conditions for the entire Simscape model to match the state it was in at a specific point you reached in another simulation. You can also use the Simulink feature to Save Final State and start from Initial State to have the entire model (physical system + controller) start from a pre-saved state.
--Steve
