I cannot make my transfer switch toggle to the utility position if there is no utility power. Likewise, it won't toggle to the generator position if there is no generator power.
One option is to make a modification to the transfer switch so you can control the low-voltage signal line that transfers the load one way or the other. I always kill my genset overnight during long outages, and use the steps as Skip describes above, but use the transfer switch to remove the loads from the genset by moving them back to utility (and then back to the genset after restarting it). I also modified the genset so I have 2 switches mounted remotely, one that controls the transfer switch, one controls the genset.
That said, personally I think its an easier job replacing breakers than it would be to replace the mechanism in the transfer switch - not that the later would be all that hard either. I just won't be doing this often enough over the life of the genset to worry about it. And its nice to be able to do everything remotely from the top of my garage steps.