The key skill in navigation is more art and less science. And that skill is orienting your map to your surroundings. There is no trick to this. It comes from practice, like so many other things. Take a chart of your favorite paddling location, and before you get into your kayak open your chart and hold it out in front of you. You will need a baseplate compass for this next step. Take a baseplate compass, and spin the rotating bezel so North is aligned with the direction of travel arrows. Then Align the long side of the baseplate with the left or right side of the chart.
So now you are standing, holding the chart flat in front of you with the compass on the side of your chart. Now turn in a circle until you 'box the needle' which means put the red end of the needle in the box on the compass. Your map is now 'oriented' to your surroundings. You can put your compass away.
Now when you look at your chart North is aligned with north in the real world. Mountains should be where mountains are in the real world, lakes and rivers as well. You can then fold the chart, put it in a waterproof map case and kayak with the chart in front of you, and keep it aligned to the world in front of you.
The Art is being able to look at two dimensional representations of land and water, and in your head convert them to three dimensional so that it agrees with what your seeing.
The key to doing this effectively is to be constantly doing it. So as you are paddling, every ten minutes or so glance at your chart, and figure out what you are seeing in the real world, and finding them on the chart. Doing that consistently is what keeps you from getting lost.
While I am not a math person I tend to think of 'lost' as an equation. It is the difference between where you are and where you think you are multiplied by time. So if you are only off by a few degrees in your navigation it isn't a problem if the error is noticed after ten minutes. Whereas after ten days, a few degrees is disastrous.
An excellent book - Deep Survival: who lives, who dies and why by Laurence Gonzalez talks about the mistakes that people make with maps and how they get into trouble. Mr. Gonzalez talks about people needing to constantly update their internal map. You can walk from your bed to the bathroom, to the kitchen in the dark without bumping into anything because you have a good internal map in your head. You can create the same type of internal map when your paddling simply by looking at a map and saying - okay this is here on the map, and there is that mountain peak.
You will get to a point - with practice - where you can orient the map to your surroundings without a compass. Simply by being able to convert the two dimensional map or chart to the three dimensional world in front of you. The more you do it, the easier it will be.
While we are talking about charts and maps (Charts show water and details with minimal information about what is happening on the land, Maps show land form (topographical maps) and minimal information about what is happening on the water. It is important to note that as coastal sea kayakers we really need both, Topo maps and Charts to fill in all the information that we need. We need charts to show us currents and depths, and tidal flats, among other things, but we need topo maps to show us good beaches where we can get off the water. When planning a trip I will use both, and when I find good landing sites or useful landmarks on my topo maps I will mark them on the chart. Then I will use the chart annotated with my marks on paddle days.
In the video below, I am orienting a map with a suunto baseplate compass. It is actually a topo map in a waterproof case from a recent trip, but the process is the same with a nautical chart. I align north with the direction of travel arrows, then align the side of the baseplate with the side of the chart, and then rotate in a circle to box the needle.