Are you talking about in the setup tab of xlights? I've always left these at 510 (or 512, doesnt really matter as long as it is equal to or greater than your (pixels x 3) it will work. Whether these unused channels contribute to performance issues or not, Im not sure.
With as many channels as your talking though, youre most likely going to be using all of them so it's probably a moot point.
In my case, I have some outputs that have, say, 50 pixels. That means Im only using 150 channels but in the software I allocate 510.