Hi Roz, Quicktime Broadcaster allows you to switch the iSight to manual focus. You can get the s/ware off the Apple site here: http://support.apple.com/kb/DL764
On load, click video tab, then options button next to iSight source, then mechanics tab.
I’ve not tried this with ISM yet, but will be trying it with the boys on our next film as we want to use the iSight to get angles we couldn’t achieve with with the DSLR.
Hope useful, iSight is a good camera and worth playing around a little with it.
I have been very happy with the Agent V6 (see: http://www.liquiddigital.com.au/). It has manual focus, shoots HD, and worked with iStopMotion right out of the box.