Hey don't worry, you can! I try to explain it.
So the Xenus's big world is made from lot of smaller levels. For example, the whole 3D world is cutted to 1 km2 parts. These parts are can be found in 'Xenus 2/lev' and 'Xenus 2/levobj' directories. A level part is not one file:
1, .lv2 file - its the level geometry
2, .ai3 file - its the AI node network of the level
3, .net file - its the old AI system's file (the game use now the .ai3)
4. wld file - its the geometry collision
5, .lvo file - its the collection objects on the level, like NPCs, vehicles, scripts, etc…
and this .lvo files are in the 'Xenus 2/levobj' path.
There are .nad and.prt files too, but I don't know what is them.
You can open .lv2 files in the Level Editor, its opens of course the other files (.ai3, .lvo etc..) with the same name, if there are. The Level Editor can do everithing with the level parts. If you just want to move an objects, because the developers has been put it to wrong place, you can do it, and you don't need to recompile the level with the geometry and everything, when the save dialog came up, you can give an option to save only the level objects and you can release only the .lvo files in the patch. So this is the level.
The .map file (needs only the world.map, the others are just test worlds) is like a puzzle game. The puzzle pieces are the "cells". A cell have an ID, a name, an image, and a path to an .lv2 file. In the original _mapplanner program its exactly looks like a puzzle. So you can take the level part's to correct place, to make a big world from little parts. The .map file also contains the missions. A mission have a ID, flags, descriptions (only for dev, can not see ingame), and mission stages, with other options, like mission text, kind of mission stage (for exmpl: Kill this NPC or Go to XY, etc) and here is the marker's source. If you have a Kill XY stage, then you have to set, who to kill. You can give the pid of the NPC (pid: The NPC's reference id on the level, putted by the Level Editor). The game will take the marker to this NPC on the ingame radar.
I hope it will be helpful, but If you have any problem with this, I can help you, just tell me what is the bug, and in what mission, and I'll fix it, and send it to you.