This is something I really have to work on. For the moment I kind of rely on the waypoints, or at least autopilot, because years of Battlefield 2/Battlefield Vietnam have ruined my helicopter flying ability.
As swimsalot said, using manual course settings is a decent alternative, and when used in concert with speed/altitude hotkeys can work pretty good.
But, after reading
Red Storm Rising again, I find myself wanting to actually fly the thing, and early tests have shown I need some work.