I used weighted baseballs (4 oz, 5 oz, 6 oz ONLY) in college and during the off-season in pro ball. I don't recommend using them in season. Just a personal thing, but it really throws off your timing. And it is VERY stressful on the arm – there's no question about that, but they're designed to be like that.
In the off-season I warmed up with a long toss first with a regular baseball. Then I threw the 6 oz ball at 75 feet for 20 throws. I threw the 4 oz ball at 75 feet for 20 throws. I finished with the 5 oz ball at 75 feet for 20 throws.
It's not glamorous or complex by any means. It doesn't have to be. 60 throws and out. Two or three days a week with a day of rest (or regular 5 oz baseball throwing ONLY) in between.
As a rule: When I started pitching off a mound, the weighted baseballs were put away till the following off-season.
Coach K's got a different program, but he's been pleased with the results, so I'd definitely "PM" him.