1. From the Energy manual, looks like you are going to have to choose either hooking the sub up to your AVR to get bass management features (important for movies and scary LFE levels), or hook the sub up via speaker wires since the manual says specifically NOT to hook up both at the same time.
If you do hook up the sub via the RCA sub input from your AVR, you won't have a sub while listening to 2-channel sources connected to the Cronus.
If you do hook the sub up to the Cronus, you could use either the variable outputs or the speaker level connections. The Cronus has Left AND Right variable outputs, but the sub only has one RCA jack - so either pick left OR right from the Cronus. You can not use a simple "Y" cable as that is for *splitting* signals - you need a *summing cable* which has resistors in a circuit setup to properly sum the signals. You'd be better off for now using the speaker level connections.
2. Yes
3. Yes you can but since the Cronus does not have HT Direct, you need to be mindful of where the volume control is set on the Cronus. You should pick a volume setting and then run the audio calibration setup on your AVR - mark where the volume on the Cronus is set and then any time you switch to that input set the volume control to that setting. This does go back to point 1 - on how you have your sub connected. If you have the sub connected to the Cronus, you won't have any bass management from the AVR - be sure to set Fronts=Large, Bass=Fronts/no sub.
4. Yes.