The logic behind the Amateur Draft is based on the draft settings each franchise has selected as well as the draft board those settings have generated.
The amount a franchise spends in High School Scouting and/or College Scouting impacts the number of players scouted from that sector. The more you spend, the more players you'll scout and the more accurate your projections will be. However, a franchise with a smaller budget can scout a player that a franchise with a higher budget doesn't. The ratio of college/high school scouting budgets will also impact the number of players chosen from that sector. For instance, if you have $14M allotted to college scouting and only $7M to high school scouting, your draft results should result in more college players taken than high school players since you'll have scouted more players from that sector. But, you'll still take a high school prospect if he's clearly better than his college counterpart. What you see on your draft board is what you should expect to draft.
The positions listed with each player is what your scouting department (HS or college) projects him to play at the big league level. For example, a better scouting department will project a SS coming out of high school to be more likely to play 3B at the big league level.
Each draft consists of the same allotment of players at each position. The quality varies from draft to draft, however.
Each draft also consists of a different set of 32 franchise draft settings. As a result, drafts vary. If everyone goes for a high number of starting pitchers one draft, then you might not be able to meet your target count because the available list of starting pitchers may be drafted.
When it comes to meeting a position target count, if the only thing remaining is partially scouted players at that position, your department will take a gamble and draft an unscouted player. This may pan out or it may not.
If a player's signability indicates he'll only sign in the first round or first five rounds and you draft him in the proper round, then he's considered a safe candidate. If drafted later than that, then he probably won't sign.
Players with leverage will ask for higher demands and take their time to sign, so don't panic. You'll always hear back as to whether they want to sign, ask for more money, or have decided to pursue another path.
College seniors that are drafted but do not sign will become free-agents the following season. First round picks that don't sign result in a compensation pick for the drafting franchise.
Currently, non college seniors that are drafted but don't sign are not in the following season's draft class. We plan on adding this at some point in the future.