The only time I've needed to do this so far was when I wanted to film at a place called Trearddur Bay on Anglesey in Wales. It's very close to RAF Valley, and in fact on the day I wanted to fly they were actually doing some training exercises.
I looked up the general number for RAF Valley, spoke to somebody who put me through to their Air Traffic Control, and explained what I wanted to do and where, explained that I would be flying below 400 feet, and approximately what time I would be flying. They had absolutely no problems whatsoever. She told me that she would make sure to inform the pilots of that fact a UAV could be flying at that time, and for them to just keep an eye open just in case. It was as simple as that.
I must say I was expecting different. In my mind I was expecting them to deny the request, or at the very least be awkward. But no, they were very friendly and helpful.