By default minimap images are located at
C:\Program Files\Eudemons Online\data\minimap
Images are TGA encoded - you can edit them with many tools, starting from PhotoShop and ending with handy and free Gimp.
Map for each area is located in a different subdirectory. You just browse through them and find which is which. For example, maps for Gobi are under 3000, maps for MistyMarsh are under 2010. There is no special knowledge why each map is in particular directory - they are just hronologically sorted as the maps were developed.
Since MiniMap has 3 different zooms, there are 3 different files - 128.tga (the normal zoom for minimap), 256.tga (zoomed in MiniMap) and 512.tga (max zoom in MiniMap as well as big map, the one you get when pressing Ctrl+M). Just put the marks where you need them and save the file. Make Backup before doing so just to make sure your image editor doesn't change image resolution and color palette making it unreadable by eo.
And, by the way - somebody was asking to re-upload boss map installation package. I found it in mailbox: