Just checked the screenshot thing with the print screen key, and my first attempt pulled the loading screen out of the buffer, and every try after that was just black like it is for you. I wonder when/why that stopped working.
As far as way points and patrols and things like that, there are a couple options. For one-time events, you can just hold the shift key to queue up movements, which works both on the system map and the galaxy map (e.g. you can send ships on a specific path through a single system or you can tell them to take a specific path through across the galaxy map jump by jump rather than the one automatically chosen by the pathing algorithm).
For stuff you're going to be doing repeatedly, you can build rally points. There's one kind that just tells units to gather at it when they arrive in the system, and there's another that redirects them to whatever point you specify, including somewhere outside of the system, so you can set up some fairly fancy patrols if you want.
Sounds like what you're looking for with the decloaking is just holding shift and right-clicking a series of points to set up paths for your tachyon drones to follow, though. Works pretty well, but their detection range is really small, so if you're really anal about finding every last ship, it can get kind of tedious relying on them. They're most useful for stuff like parking them over a wormhole to catch the ships as they enter the system so your defenses can take them out, where you know they'll definitely pass within range of them.
Edit: And of course someone beats me to it because I get carried away going into far too much detail. Heh.
