A waypoint is a position on a chart that you want to make note of. Besides for marking a position, waypoints can be used to navigate to their position.

Waypoints can be created by:
- double clicking on the Chart window when the measure or waypoint move mode is selected on the Chart Settings panel or
- pressing the "New" button on the Waypoint window or
- [control] clicking and selecting the "New" menu item on the context menu.

Once a waypoint is created it can be edited, deleted, dragged to a group, renamed or saved. All of this occurs in the Waypoint window which can be opened either by creating a waypoint (double clicking on an opened chart) or selecting the menu item "Open" on the "Waypoints" menu.

Single click to select a waypoint, then single click again a field in the Waypoint window such as "Name" or "Description" to edit it. Make sure latitude and longitude are entered as described in Position Formats. Each waypoint can also have an icon assigned to it.

An individual waypoint can be shown or not shown on the chart by selecting the checkbox "Show" next to it. All waypoints can be shown or not with the menu item "Show" on the "Waypoints" menu.

[command] click on the waypoint name on the chart to select it in the Waypoint window.
When mode is measure or waypoint move, double click on the waypoint name on the chart to edit it.

When Chart Settings "Mode" is "<+>" waypoints can be moved on the chart. Move the cursor over the waypoint name. The cursor will change to a move cursor. Drag the waypoint to the location desired on the chart.

[Control] click on the waypoint name on the chart displays a context menu with the menu items to "Goto", "Edit", "Delete" and "Hide" the selected waypoint.

If the GPS panel is opened (via menu item "Connect" on the "GPS" menu ) and a current position is transmitted from the GPS and a chart is open, you can navigate to a waypoint by selecting it and pressing the "Goto" button. This makes the waypoint active. The details of the active waypoint will be shown in the Chart Settings panel. An active waypoint can be canceled by selecting "Cancel Goto" on the Chart Settings panel. A solid blue line will be drawn from the current position to the waypoint. A solid red line will be drawn from the position where the waypoint was activated to the waypoint. Deviation from the red line is cross track error. Cross track error can be reset by reselecting the waypoint and pressing the "Goto" button.

The "Arrival Alarm" can be enabled on the "Waypoints" menu to be notified when the active waypoint is within "Waypoint Approach Distance" set in the Preferences window OR the GPS position crosses the line perpendicular to the waypoint origin line which passes through the waypoint. The "Arrival Alarm" will be enabled whenever a waypoint is made active.

The "Cross Track Alarm" can be enabled on the "Waypoints" menu to be notified when cross track error to the active waypoint is equal to or greater than "Cross Track Approach Distance" set in the Preferences window.

A waypoint is also created and listed in the Waypoint window if the GPS is navigating to one (typically done by pressing "Goto" on the GPS). When this is done a Waypoint drawer will open from the GPS panel. If the "Goto" check box is selected in the GPS panels Waypoint drawer it will become the active waypoint. When this occurs the GPS waypoint will take precedence over any other waypoint that is active.

Waypoints can be imported or exported to a file via the "Waypoints" menu and "Transfer" sub menu. For importing, the waypoints CSV file must be in the following format:

name,latitude,longitude,description <newline>
name,latitude,longitude,description <newline>

latitude and longitude must be in the same format as the selected Position Format

OR they can be imported or exported as a CSV file or a GPX file or a Google Earth KML or KMZ file. Dragging a group to a Finder folder will create a GPX file. Waypoints can be transfered to X-Traverse.

Waypoints can be copied to and from the GPS via "Transfer" sub menu item with the menu item "To/From GPS" via the "Waypoints" menu. Currently Garmin, Furuno, Magellan and Other protocols are supported. Before the transfer begins the GPS panel will automatically be closed. Make sure the correct brand of GPS is selected in the GPS Settings drawer. Garmin GPS will need to be put in Data Transfer/Slave or 'GARMIN' Mode before a waypoint transfer can be performed. Other GPS must support the $GPWPL NMEA message. Since GPS's don't support long unrestricted waypoint names or descriptions they will be reformatted and truncated when being transferred.