1. If you're using linux then, download a copy of your mapcache.dat then open weemapcache and open your mapcache.dat.
2. Click FIle on Weemapcache then select your custom map's gat file then hit Save.
3. Upload your mapcache.dat to your svn (db/re or pre-re), overwrite the file.
4. Open map_index inside the db folder, then add the name of the custom map at the bottom, must follow the instructions there.
5. Same with conf/maps_athena.conf, you must add the name of the custom map and instructions should be followed there.
6. Upload all the custom map's files in your grf file(Your Custom GRF).
After following these instructions, you need to re-compile and restart your server. Congratulations!
Mosaic's post in how can i install custom map ? was marked as the answer