Okay gang, it works. I've got it so the map folder will show the Peat Bog, including mostly-accurate "You Are Here" arrow.
1- Get a map and convert it to DDS format. ***The actual map area needs to start at 0,0 and end at 436,506 or it will get cut off!*** The image itself should be 512x512.
2- Find the "internal name" of the zone. You'll need to find it under the "paks" folder. Example: The Peat Bog's internal name is qey_adv04_bog
3- Duplicate one of the Image Styles under MapStyles and rename it to the internal name of the zone.
4- Set the ImageStyle's zonerect to reflect the loc of the upper left and lower right corners of the map. Switch the negative/positive values for the X axis.
Example: Map of the Peat Bog here:
http://www.***************/eq2/maps.asp?ID=7
You can see that the NW corner's loc is labelled 850,345, and the SE corner is 545,670. Therefore, the zonerect for qey_adv04_bog is "-850,345,-545,670"
5- Go to MapPage and it's subpage Icons. You'll see here that there's a Page with each internal zone name just like there was an ImageStyle in MapStyles. Duplicate one and rename it to the zone's internal zone name. Now you can create/move/rename the "points of interest" icons for that zone.
(When placing markers, go to the image "ZoneMap" and change it's style from "MapStyles.fprt_hood01" to "MapStyles.(currentzonetoedit)" to display the map in the editor window.)
The hardest part is going to be getting the ZoneRect 100% accurate.
Unfortunately there doesn't appear to be a way to do anything with the height axis, so Eloa's method will probably still work better for multi-level but single-zone dungeons like Blackburrow.
Edit: Ooh! He could use the method he's doing to show/hide images underneath the regular map area, then use blank maps. That way you can sort through multi-level dungeons AND have an accurate loc arrow!
Note: I'm saying "arrow" instead of "dot" because that's what's currently on test and it should be live within a week.