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Once a player is drafted a scout or director will call the player and a signing bonus will be offered. The player can negotiate this himself or have his agent do it.
Signing Bonuses are usually determined by the round that the player was drafted in. You can usually get a good idea from the previous years draft signing bonuses for what the "slot money" is for where you got drafted.
First round draft picks are usually in the low millions of dollars. They can get up to a few million for the first few draft picks and down to just under a million later in the first round.
The higher the round, the lower the signing bonus will be (usually). There are a few things that can keep you from getting slot money. If you are a senior in college you will usually get less money because you have no options. Either you sign, or you go play independent baseball. The clubs hold that over you and can give you less of a signing bonus because of it.
Another reason you may not get slot money is if your grades are bad. They can do this because of the same reason they do it to seniors. If you are going to be ineligible the next season, you really have no choice but to sign so they offer you less of a signing bonus.
Once the signing bonus is negotiated. The player will sign a Minor League contract in which they will recieve a salary on top of their signing bonus. The Minor League salary is significantly less than the Major League minimum salary.
When scouting for professional players, scouts will try to find out a players "signability". Signability is how able and willing a baseball player is to sign a professional contract and for what signing bonus will he be happy. Sometimes less signable guys get more than slot money because they are great players and clubs want to persuade them to sign.
On the other hand, sometime less signable guys get over passed because clubs don't want to over pay or hassle with someone who is not worth it. This is why having an agent is a good thing. They can honestly asess the situation and negotiate for the money you deserve.
Also check out this related article called Signing A Professional Baseball Contract