I sort of cheat by generating my planetary maps using the Civilization 3 map editor, which does give a bit of different results in terms of view, but also gives a grid coordinate system. I generally do not use the grid system though, but start naming continents and islands, locating and naming cities and towns, along with other major features, which then gives me the ability to locate things on the map.
Now, here is the system I am thinking of to use for the Marooned and Marooned Alone Adventure, for which I have the hard copy book and digital copies. I was thinking about printing two maps using the digitial copies, and leaving one untouched. On the other, I am planning to label various areas, such as deserts, mountain ranges, seas, rivers, North and South Poles, add any additional cities/towns/villages, forests, jungle areas, etc. so that I can orient myself on the blank map based on the notations. The center horizontal line is the Equator, while the two other horizontal lines mark the 30 Degree North and the 30 Degree South parallels.
Then I can say that the group in the life boat landed in the forests just south of the Scylla Inlet on the Sicilian Sea, while the lone adventurer landed in the plains just to the north of the northern tip of the Sicilian Sea, thee hexes east of the Tiber River and Etna Mountains. Now, if I really wanted to do things right, I would pull the map into Photoshop, and add all of the various labels with the text editor.
I have not tried to do this with say, the Victoria map, in JTAS Two, but as that already has a fair amount of names, adding additional ones should not prove problematical. This approach does work best with a planet with a range of terrain features, so it would depend a lot on the planet being mapped. However, by keeping in mind the 30th Parallel lines, designating a Prime Meridian, and an opposites 180 Degree line, preferably each on one of the triangular tips, you can then figure that each tip of a triangle represents a 36 degree shift from the tip of the next opposing triangle pointing either north or south. Then the 45th Parallel will run halfway between the equator and the respective pole. If you designate the Prime Meridian at running along the right hand side of the map as you look at it, then the 180th Meridian will be in the center of the map. Then the tips of the northern triangles would be located at 72 degrees and 144 degrees west, and the tips of the southern triangles would be at 36 degrees and 108 degrees west.
Now, looking at the map of Pagliacci in Marooned, the life boat comes down in the hex at about 48 Degrees South and 175 Degrees west of the Prime Meridian.
What I might have to do is try to get my ideas into Photoshop with a map, and lay them out visually for everyone to see.