I'm working on the Isle of Minocra map and thought a quick tutorial would be useful.
For this project, I'm using MapGen2 to create the initial map, then importing it into Photoshop where I'll superimpose one of my hex templates and add symbols.
I'm assuming you have some passing familiarity with MapGen2 and how it works. The trick is getting a screen capture of the map you want. I've tried several monitor resolution settings to get a decent on-screen size, but as long as the capture is square (i.e., same width and height), you're fine.
Use the MapGen2 tool to create a map.
Select "Perlin" from the Island Shape section.
Click the "Random" button until you find an island shape you like.
Select the "2D Slopes" view.
Use a screen capture tool to copy the map image and convert it to PNG format.
I'm assuming you are using Photoshop. If you don't have Photoshop, you might try GIMP, which is free, and (as I understand it) supports many Photoshop-like features.
Create a new image that's 8.5" x 11" and 300dpi (you want the high-res so that you can read the hex numbers later). Leave this image open in Photoshop.
Open the desired hex template in Photoshop (note: the PDF versions in the hex template download are 300dpi, so they'll work fine).
Drag the hex template's "Background" layer into the new image.
Open the MapGen2 image in Photoshop.
Drag the map's "Background" layer into the new image.
In the new image, re-size the map image to fill the hex template.
Move the map image layer (Layer 2) below the hex template layer (Layer 1). The hex template will cover the map image.
Select the hex template layer (Layer 1) and change it from "Normal" to "Multiply." This will make the white background of the hex template transparent so the map image shows through. 
Save the file in Photoshop's native PSD format because you want to preserve the layers. (The file will be big (~41 MB) because it's hi-res—if anyone knows how to make this file smaller, please share the knowledge.)
Most mapping software packages include symbols. And, truth be told, most of these symbols are pretty good. However, if you're working with image software to produce your maps, it's best to have your symbols in the form of a font. This saves you the time of creating them yourself, and they're easy to replicate with precision from map to map.
Download and install the Carta-Normal TrueType font [see footnote #2 for links] N.B. Before the font shows up in Photoshop, you'll need to save your work, close Photoshop, and re-open your map.
To place a symbol, select the Text tool and switch to the Carta-Normal font.
Type the letter or ALT-key combination of the symbol you want (see the Carta Normal Symbols PDF at right). Photoshop creates a new layer automatically, which I name after the hex number, but you can use whatever naming system works best for you.
Select the text and adjust the point size and colour to make it stand out on the map (I recommend a red, yellow, or orange to make it easy to see against the map background).
Select the text layer you've just created and apply an Outer Glow layer style.
In the Outer Glow style dialogue, change the Blend Mode to "Linear Dodge (Add)" and choose the "Foreground to Background" style from the Gradient Picker. This outlines the symbol with a white highlight.
Continue placing symbols on your map repeating the process at Step #3, above, until you've placed all the symbols you need by copying an existing symbol, moving it to a new spot on the map, and changing the character. This preserves the formatting and helps keep your symbols consistent. If desired, add a map key that describes what each symbol is (though you can easily refer to the Carta Normal Symbols PDF).
Last, if you're into the OCD, don't forget to label each symbol on the map (for random names, I like EBoN for its large number of culture libraries). Maybe draw a road or two. Whatevs.
This is a quick and dirty tutorial (written by someone who's not a Photoshop wizard). I'm certain the experienced among you can devise some shortcuts to reduce time spent (not to mention filesize), but this should be enough to get you going.
Next up, I'll provide short descriptions for each location on the map, in a style that fits your busy GM schedule.
This is a freely available font that (as far as I can tell) you're free to use in your commercial work. Since this article's publication in 2012, the original source link is no longer active; I'd suggest searching for "carta-normal font" in the Googles. But if you're feeling lucky, here are some sources (current as of 8/26/15): Fonts2U, FontZone, FontPalace, and FFonts.