WithADanceNumberJust like learning anything else. You gotta put the time in. I personally think that pubs are really good for just grinding out aim (just dont sit a million miles away, keep yourself pressured). If you are a 6's player then go sniper when your team needs one and practice a bit there, just remember to switch off when appropriate.
Also i really like the muscle memory room in this map, http://tf2.gamebanana.com/maps/104304 When I snipe I typically aim for center mass of my enemy then flick to where their head will be (helps me with movement prediction).
This. One of my favorite things about Sniper is that clicking heads is more or less the same wherever you go. Pubs are just fine for practice but only if you treat them right (aka don't only snipe snipers and spun-up heavies, don't stand around in 'sniper spots,' don't bait the fuck out of your team for easy kills on other snipers). DM is really useful for learning to deal with competent players, like finding intervals for a clean shot between spam, identifying strafing patterns, and hitting jumpers who can actually airstrafe.
My preferred point of reference is anywhere to the lower right of the head. Flicking up and to the right is much more reliable for me. If you see good snipers rescoping, it's because they're trying to find a good point of reference before taking their shot. If you start noticing yourself use one, then you're making good progress.
Also that map looks neat I'm going to try it.