The check in time doesn't really affect the network as much, as it's a comparatively small packet. However, it can overload a NS server pretty quickly with requests for updates, especially if they don't need it.
I would, if possible, use the AD Import to automatically set the sites\package server relationships up.
Finally, I would set the throttle to specific speed over a %. What the % does, is during package download, it sends ping packets out repeatedly to determine what the threshold is, and where the download fits into that. So, in my opinion, you actually add MORE overhead by using % vs. a specific download limit.