Okay, first of all, all grounds should be tied together in any box. The exception would be when using isolated-ground receptacles, which are a 100% waste in a non-metallic wiring system.
In other words, if you're using NM cable and plastic boxes, the ground wire is already isolated. In a metallic (i.e., metal conduit) system, the ground wire should be insulated and grounded only at the origination panel.
As for shared neutrals, the circuits must be on opposire phases. The two breakers need only be tied (i.e., a 2-pole breaker) if they're feeding a single equipment, or if they're feeding devices on a single mounting strap.
If two separate breakers feed two separate circuits sharing a neutral, when terminating the neutral at, say, a receptacle, the neutral must be spliced and pigtailed, not joined via the two silver screws on the receptacle.
This is because, since the two breakers are not joined, if someone turns off one circuit to replace a receptacle, the other circuit is still energizing the opened neutral through its loads, which is obviously dangerous.
Once leaving the panel (or a junction box with a 3-conductor cable feeding in and two separate 2-conductor cables leaving), two separate circuits must remain separate; in other words, never rejoin the two neutrals downstream.
If two separate 2-conductor cables are feeding several devices in one box, the neutrals should NOT be tied together. Treat them like two separate circuits. And never use one circuit's hot and another circuit's neutral.