Not sure what you mean by "it makes no difference"; every battle you win ramps up your enemy's war exhaustion. Invading and occupying planets augments war exhaustion pretty heftily, although you actually have to invade the planets, not just park your fleets in the same general system. In my experience, with a proper war goal set, it doesn't take too long to drive war exhaustion up.
Unless you're gunning for total conquest or something like that, in which case, good luck. You pretty much have to occupy all of their planets with invading armies.