setup

you first need to have installed this addon in Garry's Mod either via Github (in the garrysmod/addons folder) or with Steam Workshop

you'll then need an image editor such as Aseprite, Krita, GIMP, Affinity Photo, paint.NET.. actually, I personally use Aseprite which is for pixel art (since we need to edit raw pixels, it's a nice choice) but I used to use GIMP and it worked well enough, so you can use any software you want. I'll assume you already have basic knowledge about how to use one of them.

generating
so.. how to make a minimap? we could draw it by hand but it would take sooo much time and the result may be bad, that's why I coded a simple command in order to make a base texture to work with, run Garry's Mod and follow these steps:

launch a singleplayer game by choosing the map you want
enter guthscpsnav_generate in your game's console
tweak the values in the panel to change the height region to capture
press the save to data button
find the generated texture file at garrysmod/data/guthscp/snav/<map_name>.png
using the minimap generator: image

generated texture: rp_site48_v2

image editing
this is the most boring part: editing the generated minimap to make it look like a S-NAV map

setup
first, open the generated texture in your image editor, you'll see that the map void is black and all buildings are transparent (thanks to a bug in my minimap generator), which is quite nice, because we have less things to do (like removing all the colors..).

you should now follow these steps:

(possibly) fill with black all non-desired locations (like admins zones, 106 dimension..)
shows only the map walls
select all black pixels (disable 'Contiguous')
shrink your selection by 1px (usually in 'Select' tool list)
delete selected pixels
(possibly) reveal some hidden areas by creating an inside 'Outline'
see the in-game result
save the file in garrysmod/materials/guthscpsnav/minimaps/<map_name>.png or, if you're making an addon/map, at garrysmod/addons/<addon_name>/materials/guthscpsnav/minimaps/<map_name>.png
restart the singleplayer game
equip and activates the S-NAV
perfecting the image
walk around in the map and compare the minimap with the world
remove incorrect or add needed pixels
save your changes, this will automatically updates in the game
see the in-game result
repeat.. again.. and again..
already finish? yeah, publish now!
final result: rp_site48_v2