I am new to this. Question  The amatuer draft will be soon.  There are not but 500 amatuer players to draft from.  Where do we get the other  300 or so players for 32 teams to have 25 rounds of drafting

You do not see everybody, you will only see at most 500 players based on your scouting budgets.  There are enough total players in the pool for the draft.

Honestly, you won't care about the last 10-15 players you draft. You should probably still sign them to fill out your rookie league team, but the cost will be negligible and you will eventually end up cutting them after they've moved up through A ball. If you're lucky, one of them might turn into a diamond in the rough and help you down the road.

You will want to manually rank the first 50-100 players, which should take you through the first five to 10 rounds, depending on your scouting budget. Simply put, move up the players whose skills you value and move down the players with fatal flaws (lousy splits, for example). Pay close attention to the top 25 players, and worry less about the players after that.