These are settings which affect how Apt itself behaves. You can access this form via Menu->Apt->Settings on the main form.
To enable 5-way navigation support, press left, right or centre on the navigator pad. Once enabled it will remain until you exit Apt.

Enabled checkbox
Whether Apt is currently enabled. If disabled, it will never affect your device operation.
After Reset checkbox
Usually Apt will be disabled after a reset. To automatically enable after a device reset this should be selected. You should experiment with the application to be sure it doesn't cause problems before selecting this.
Note: your device is very busy after a reset. Even when the first app UI appears your palm is still likely to be processing for a second or two, and during this time Apt settings have likely not yet been loaded.
Apt Priority
If several applications want to handle a hard/soft button press, this setting can have some influence on which one gets it. A higher priority means Apt is more likely to grab the press.
Repeat Time (MS)
When holding a hard button, rocker switch etc, the number of milliseconds before the next repeat count
Min Press(MS)
The minimum number of milliseconds a key must be held to match a repeat value 0 trigger. This setting can be useful for compatibility with other button handlers. If you are not using another button launcher, it should be quite low so that Apt can quickly respond to press-and-release (repeat value 0) triggers.
Pen Acc. (pixels)
The length of the sides of the square for catching strokes and taps. If stroke coordinates overlap, it may cause problems with e.g. double taps being detected as strokes. This should only be the case for relative strokes. In any case, a warning is given if changing of Pen Accuracy results in overlapping catch areas of relative or fixed strokes.
Macro Delay
This will in general speed up and slow down execution of macros. Do not expect the values to be be precise measurements of anything in particular. If you are having trouble with e.g. macros not completing, you may wish to experiment with different values. Note: some steps in a macro will take time for the OS to execute, whatever value of Macro Delay you have set.
Bright Restore
This setting is intended as a safety feature, though it can also be used as part of a brightness dimming strategy.
If a value is given, then whenever the screen brightness gets equal to or below the value set, any hardware
input (button, pen tap) will result in a Bright:Restore action and the input will be ignored. It can be thought of
as 'waking up the screen when it goes to sleep'. A good possible power saving method is to set this value to
0, and have a Brightness:Set:0 action have a certain amount of Idle seconds.
Use Default Prefs checkbox
Apt's normal operation is to apply a target's prefs if there are any, and otherwise to use the prefs from *Default*. If this checkbox is disabled, Apt will record the prevailing prefs whenever a target is loaded that has a preference block, and restore the recorded prefs when a target is loaded that does not have prefs. That is slightly (though probably imperceptibly) slower.
This setting applies only to the prefs from the Prefs screen.
Use VFS checkbox
Enable/Disable external memory card support. See here. Only possible if your device supports external memory cards. When you change this setting, Apt will automatically relaunch itself, please don't be surprised :-)
Show Hidden checkbox
Whether to show applications in the target selector that have the Palm hidden attribute set. When you change this setting, Apt will automatically relaunch itself, hold on to your seat.