I was always taught when stopped at a station you should have the automatic brake valve in suppression, the independent fully applied and the throttle in idle. Never run a train with a manual lap brake but the above should hold true whether in direct or graduated release.
When it comes to stopping the train direct release or freight brake vs. graduated release or passenger brake are two completely different animals. As explained above, with direct release you could in theory make a 10lb reduction then manipulate the throttle back to idle to make your stop possibly adding a little more air as needed. This type of braking in modern passenger service is frowned upon except in very few places like Auto Train.
Graduated release allows you to manipulate the brake to add and subtract air to make you stop. But air on a train is not a constant. The more you manipulate the brake valve the less air you have in the system.
Then of course there is a third option called dynamic braking for slowing your train if the engines are so equipped.
Green means GO Red means STOP Yellow your on YOUR OWN