A few tools I use to generate geodata.

Use L2MapConv to generate the geodata file in l2j format. (make sure the .unr file is encrypted, you can use l2encdec for that in the case of a custom map.)
use HDG Editor to convert unnecessarily complex blocks to simple blocks (this is done autoamtically when you load the .l2j file and re-save it.)
Use L2J GeoEditor to automatically check all blocks and convert them to Complex, if necessary.
Lastly, use G3D Editor to manually fix the geodata.

I don't think adding a guide is necessary since the whole process is pretty intuitive.

You need JRE 1.8 for all of these tools.

Credits go to the original authors of each program; i did NOT make any of them.
(G3D: https://www.l2jserver.com/forum/viewtopic.php?t=21432)
(HDG: Created by humordwarf, edited and optimized by DRiN)
(L2MapConv original repo: https://github.com/m49n/l2mapconv-public)