"Electrically" the grounds are all the same. With that said, there are times when it's best to tie the ground directly to the battery (often with audio ground-loop issues) and other times when it's best to tie it to the chassis. That's a rather ambiguous answer, I know, but in the case of a Cap, I believe either will work. If you haven't already purchased both, you MAY find that one or the other may solve any issue that you may be having that requires them (if you just need more power a second batt. can help, if your lights dim on big bass hits a Cap may help, I'm sure Soundman will have a better answer here but I've seen more and more competition audio guys moving away from caps and toward high capacity, quick discharge batteries designed for car audio).
As far as not needing a H.O. Alternator with the addition of these two, that may be true.... or it may go the other route and make the need for a bigger alt. even greater. It depends on how you use your system. I have a second batt. setup in my Jeep. When the Acc. circuit is on, they are connected through a solenoid and they disconnect when the Acc. circuit is off. This way, the PC, Amps, Scanner, etc. (connected to the Second Batt. side of the circuit) is normally powered off both batt.'s and the alternator when the Jeep is running but can also be ran off the second batt. alone when the vehicle is off. The only issue with this, which may affect you and is why I mention it, is that if you run your system off the second battery for a while with the truck off, when you turn it on and charge the second batt. off the alternator it creates a big draw on the primary battery and the alternator. Over time this may wear out your alt. and require replacement.... but then again the way I see it, you can run off the factory alt. and see what happens. If it dies, replace it with a bigger one, and if not, that saves you some cash. The risk is that one day, your truck might not run (if the factory alt. dies) and then you'll have to wait on a new unit to arrive.... just gotta weigh the risk.