For JJ2 if you minimize the game it will stop eating up your CPU. You can't do this when hosting, and when playing online you will CTO. But if you're finding that it is slowing down your computer (such as by making programs take forever to load or do anything), then this will help. There are also hacks which allow you to minimize while hosting and not have any problems, but I do not know where to get them any more.

As for JCS, it's not THAT bad of a resource hog. If it's showing 100% cpu use, it's because there is nothing else running besides JCS that needs the CPU. If you have a computer that has cooling problems or a laptop with a weak battery this might be a problem, but otherwise it shouldn't bother you. Just close JCS when you aren't using it. Also, you might want to try zooming in to 100% when leaving it idle. The zoom level is basically the #1 factor that determines how many resources JCS is using. At 12.5% zoom you will notice a much more significant slowdown than you will at 100%. I believe minimizing might also help with JCS, but I'm not totally sure on that.