The roster order doesn't affect anything in the game; it merely sets the order that players are shown on the roster and box scores. It really doesn't matter how you choose to order your roster, however, since the only effect is how your roster is shown and the order of players in box scores. Thus whatever you find the easiest to read is what you should use.
For each position, you must list the starter and two reserves (one for catcher). The starter will always start if healthy, otherwise the first reserve, otherwise the second reserve. To facilitate platoon assignments, you must enter two sets of defensive assignments -- one to use against a righthanded starting pitcher and one to use against a lefty.
The defense screen also gives the opportunity to set defensive substitution priorities. You should do this in order of decreasing defensive prowess, as a player higher up the list will be inserted late in a game to try to hold a lead.
As with defense, you give two sets of batting orders. One is used vs. righthanded starters, the other vs. lefthanded. The players specified in your batting order are merely the selected starters at each position in the defensive orders; thus you should set your defensive assignments first.
You also select pinch-hit lists for use vs. righthanded and lefthanded pitching. As opposed to the other dual lists, the PH list used by the game is the one for the handedness of the current pitcher rather than the starter. A player higher on the list can be used to pinch hit for a player further down the list. The pinch hit list also determines the designated hitter; the DH is the player highest on the PH list who is not starting on the field. Note that the DH is used in all games other than NL home-field games at AA or higher. All college games also include a DH.
Your pitching controls allow you to set your starting rotation and "depth charts" of various reliever classifications.
Your starting pitching is a rotation, in that pitchers start in turn beginning with the first. Thus if you have five pitchers listed in your starting rotation, each man will start every fifth game. If you have four, each starts every fourth, and so on. In the starter controls, you can also specify which starter is next to start, as well as the "pitch count". Pitch counts are specified by the number of days to return to 100%. A 6-day pitch count, for example, ensures that the starter will not become so fatigued as to not be rested after 6 days. (This corresponds to a 5-man rotation with a day off.)
The other pitching lists are priority lists. If you are in need of a long reliever, the game will pick from among the players listed in your long reliever list, considering position in the list and fatigue level. The same is true of the other assignments. One special note is that mopup relievers (used in blowouts) are preferentially taken from the bottom of the long relief list.
The bulk of the coaching options controls are dedicated to determining how your team plays in various situations. All of the options determine how likely your team is to do a certain thing, such as bring in a pinch hitter. The options range from least to most, with normal being the middle option.
Two options pertaining to bullpen use could likely use elaboration. "Hook" determines how quickly the starter gets pulled. The game automatically considers fatigue, so the primary variable is the number of runs allowed. A high value will bring the starter out quickly after giving up a few runs; a low value will leave him in.
The second option is relief pattern, and has four possible selections. Standard refers to standard bullpen use: closer in the 9th inning in a save situation, setup relief in the 7th and 8th inning, and long relief otherwise. Sabermetric refers to a pattern recommended by statisticians, in which better relievers (closers) are used preferentially with 1-run leads or tie games, setup men in other high-leverage situations, and long relief otherwise. Both options can be used with or without "lefty one-out guys" (LOOGy), pitchers brought in to face one batter to exploit a handedness matchup.
The other main option in this control screen is game training. Game training gives your players temporary ability boosts (for the game only); you can divide up to three points between batting, pitching, and defense practice. Points are counted separately for pitchers and position players; both sets of players take defense practice. Be adivsed that the more points used, the more fatigued your players start the game.
In college, you are allowed to designate players as redshirts. A redshirted player will not play in a regular game (he can play in scrimmages or exhibitions), but will gain an extra year of elibility. A player cannot redshirt if he is a junior or senior or has already redshirted a previous year.
In the pro game, you can assign a captain and an assitant captain. These settings are primarily for show in baseball.