Shawn, I have had alot of success using weighted baseballs. I have also had alot of success training high school shotputters and discus throwers using the exact same methodology.
Im not sure if anybody has touched on this aspect of "the thought process" or "concept" behind weighted baseballs. In order to throw harder several aspects have to be overcome. This is true regardless of using weighted baseball, there use helps incourage a response. Im talking about a neural response. Before one can throw harder he first must prove to his brain that he can do so without injuring himself or that his body can withstand the stress. THe body is pretty good at limiting itself in regards to certain motions under the guise of protection. A good example of this would be the bench press. When benching the last 40% to 50% of the lift the arms are actually slowing down in speed, one cure bech throws with a med ball which is a balistic approach. Im sure for more than a couple of reasons, obviously gravity plays a role. The brain also is slowing the arms down in order to proctect the body from potential injury. Or max running speed after a certain threshold is reached the body will not alow the person to go faster. Could be a strength/flexibility issue or mechanic issue either way the body is going to put the brakes on. The body is an incredible machine that recieves signals from the brain and promotes action and sometimes inaction or limited action, this is why balistic training is good . Another example which is perhaps the most general could be when you feel the pull/stretch at the end range of a motion in part those signals are telling you to stop if you dont stop the motion you will probabaly pull a muscle or perhaps damage a ligament.
The point Im making with weighted baseballs is this. They are NOT intended to be used in a manner that is RAMPED up all of the time. Save that for the 5 ounce ball later on, especially in younger guys. Think in terms of increasing "cruising speed". The ability to measure speeds with radar is key when using weighted balls. Have your pitchers throw a 5 ounce ball with near full max intent, measure the speed. Than tell the kid to think in terms of "taking something off" or " not going all out" use any words that PROMOTE the RESULT of around 85%to 90% percent of full near max throws. The purpose is to find out what his cruising speed is with the 5 ounce baseball. This is than called the "target speed", the speed at which hes cruising. Its important that he learns to feel what this is, thats why radar is important you need the feedback and guessing will not cut it. Once you identify this cruising speed and he repeats it than incorporate the weighted ball and he throws it with the SAME EXACT EFFORT. Of course you will see a drop in velocity due to the extra weight of the ball. After enough throwing is done using the different weighted baseballs, the 4 ounce ball too to promote arm speed you will find through using these balls with the SAME effort that eventually he will also throw the weighted baseball with the same speed he did with the 5 ounce ball while throwing with the SAME INTENT or the 5 ounce ball as fast as the 4 ounce ball. One reason for the adaptation is for lack of better explanation your in a sense "tricking" the brain to think it is still throwing a 5 ounce ball when in fact it is throwing a heavier ball, this in part is a neural adaptation that is inherent for increasing velocity. As far as amount of throwing as well as frequency this has to be adjusted to the individual. I would excercise great caution with the younger guys, doesnt mean they cant but certainly no wheres near what am older person would do numbers wise as well as intent.
After training within this protocol than you find out which area needs to be addressed as far a strength goes, CaDad made a reference to this in another thread that was deleted by somebody. After leaning what the exact cruising speeds are through trial you may find that the kid is closer to his 5 ounce ball speed in regards to percentage of difference between the heavier ball and the lighter ball. This will help in determining if its arm speed he needs or arm strength he needs, the fact is both of these force and velocity are so intertwined that they should be addressed keeping that in mind, as force goes up velocity goes down and vice versa . One facilitates the other. I hope this helps you understand some of the concepts behind their usage.