Reordering mods is done in the GameUserSettings.ini file, there is an option called ActiveMods which contains a list of ids separated by commas.
To change what order the mods are loaded in, the ids of the mods just need to be arranged in that list.
The easiest way to find what order mods need to be in is to go onto their steam workshop page and take a look at the icon, if there is a green puzzle piece then the mod can be loaded in any order. If there is a yellow puzzle piece then the mod must be loaded as far to first in the list as possible. Some mods require to be loaded before all other mods, such as maps, total conversion and annunaki genesis.
For example if i wanted to load Valhalla (504122600) and Annunaki Genesis (538986229) onto a server the ActiveMods option would look like this:
Since Valhalla is first in the list, it will be loaded first when the server starts - before Annunaki Genesis.
If Genesis was loaded before Valhalla the server may not start up.