Waypoints are spots you choose either out in the field with your GPS unit that gets uploaded to the map on your computer later or you can maneuver to a point of interest such as a depth of lake, a shoal, mouth of a brook etc with your GPS' cursor, mark it as a waypoint and upload it to the computer.
Either way, you need the handheld to do anything with it.
I'm taking my PN-20 onto a lake for it's first time this morning. If we have a hot trap I'll mark it's coords as a hotspot.