Tonight I tentatively/experimentally placed signals around the South Upton Wye (in the proper places according to track maps of course), and so far they work! All legs of the wye here were controlled by the tower to the west.

In this example here, a train from Milwaukee is coming towards the camera, and a Mundelein-bound train is waiting to cross over to head west.

After the Chicago Limited clears, the Mundelein train gets the lineup.

This has just been testing in Freeroam. I have yet to try it in regular scenario. Hopefully it will work when it comes to that, and hopefully this bodes well for signalling the rest of the route!
Zach