Initial Time represents the base time each player has at the beginning. This can be adjusted specifically for player #1 or #2 by using Handicaps. For each player, that player's handicap value is subtracted from his or her starting time.
So for example, let's say that the Initial Time is set at 5 minutes, 30 seconds. If Player 1's handicap is set for 1 minute, 45 seconds; and Player 2's handicap is set at 0 minutes, 0 seconds - then when the game starts, Player 1 will start out with 3 minutes, 45 seconds; and Player 2 will start out with 5 minutes, 30 seconds.
Fischer Time is primarily a chess concept (though of course it can be used in any game). The idea is that every turn, x seconds are added to your clock. For example, let's say this value is 20 seconds, and player 1 begins at 5 minutes and 0 seconds. Player 1 starts, takes 5 seconds for the first move, and hits the "Switch" button. Player 1's time is frozen at 4 minutes, 55 seconds. Player 2 takes their turn, and after 13 seconds hits the "Switch" button. Player 1's clock resumes counting down, but now starts at 5 minutes, 15 seconds - 20 seconds was added. When Player 1 hits the "Switch" button again, Player 2 will resume at 5 minutes, 7 seconds. This value defaults to 0 seconds (in other words, disabled).
The above example assumes that the Apply at end of turn checkbox was not checked (the default). If this box is checked, then the extra time is added at the end of each player's turn (instead of the beginning of the next turn). So in the above example, when Player 1 first hits the "Switch" button, Player 1's clock immediately increases to 5 minutes, 15 seconds, and is frozen there until Player 2's turn is over.
Reset timer for each turn defaults to not checked. This default behavior means that, with the exception of Fischer Time, once a clock has wound down, it doesn't go back up until the end of the game. If this checkbox is checked, that means that at the start of each turn, the active player's clock is reset to the original value from the beginning of the game. So if each player starts at 5 minutes, 0 seconds, and Player 1 takes 4 minutes and 59 seconds for the first turn - when Player 1's second turn comes along, he or she will have 5 whole minutes again.
Note that Reset timer for each turn overrides Fischer Time. That is, if Reset timer for each turn is active, then Fischer Time will have no effect.
Use Hardware Buttons means that no buttons will be shown on the screen - instead, players are expected to use the physical buttons on their Palm device. Specifically, the Calendar button is Player 1's "Switch" button; and the MemoPad button is Player 2's "Switch" button. Either hardware button may be used as the "Start" button.
Unless you have installed another utility on your Palm device to disable this feature, most Palms are set to turn themselves off after some amount of disuse - usually 1-2 minutes. Checking the Disable Auto-Off box will prevent the Palm from shutting itself off automatically while either clock is ticking. (Note that if the clock is paused, or if the game is over or has not started yet, neither clock is ticking and therefore after the normal 1-2 minutes the Palm will shut itself off.)
Accuracy is a value between 1 and 100 which balances how often the clock display is updated vs. your Palm device's battery conservation. A lower value (1) will be more accurate, but will drain your battery more quickly. A higher value (100) will be less accurate, but will preserve your battery better. Note that in either case, the clock is equally accurate, technically - but too high a value may cause the clock to appear "jumpy," with more than a second going by, and then having the clock's value jump by several seconds. This value defaults to 10.