I'm planning to build a big play shed / garden office when the new house is finished. Overnight, a couple of 1m2 sealed double glazed units appeared next to our skip. As they're free, I'm going to put them in the roof of the shed. The roof will have a slope of about 1 in 20 to match the existing garage which is next to it. What's the right way to waterproof windows on a flat roof? Vertical windows don't have water sitting on them so nothing special needs doing. Velux windows have special flashing kits to go under tiles, and anyway you can't fit those at less than about 15°.

I'm going to make the frames so I can do whatever is needed. What do I need to do?

Google through some images will be better than me trying to explain. Pick a design that lends itself to what you have in mind and try to replicate it.
https://www.google.co.uk/search?q=flat+roof+skylights&client=opera&biw=1385&bih=881&source=lnms&tbm=isch&sa=X&ved=0ahUKEwj Xm-7RqMTOAhVkBsAKHQbbBogQ_AUIBygC

You'll never manage to get a standard unit watertight sitting flat, as the water will pond in the unit and it'll be a water of time before the seal of the window packs in.

what roofing materials are going to be used?

Cheapest option would be to box profile sheet the roof with some clear Perspex sheets put in every now and again to let light in, if there is enough pitch/ run on the roof.

A slope of 1 in 20 should be plenty to stop the water pooling. Some of the pictures on google images show the bottom edge having no lip on it, so the water drains off. Also most of the pics have the window raised above the roof on a lip. Presumably to stop water on the roof from getting in.