Version 1.4 of the plugin was just released which plays nicer w/the 3.5 media handling. Note that multiple post thumbnails (MPTs) don't use the media modal like the featured image does in 3.5 but still uses the old style thickbox chooser. The main change re: 3.5 media handling is that when you are choosing a featured image, you won't see the MPT choosers in the image editing fields in the sidebar.
The other change in this version is to use a context parameter to only show the thumbnail link that was clicked on to invoke the thickbox when the attachment fields are shown w/the link to choose an image as your addt'l thumbnail. This reduced confusion and clutter when more than one MPT is registered.