So here is whats going on:
When using Steam mods they are automatically loaded at the bottom.

Normally mods load by folder name in alphabetical order so A loads at the top and z loads at the bottom.
This is one way to organize mods without needing to manually do it.

The issue arises when using Steam mods and manual mods. Manual mods follow the same structure but for some reason Steam mods are always loaded AFTERwards and also the same structure but by using mod number (I'm pretty sure its the number but could be wrong).

This makes it impossible to save a load order.

Well I come to help!

After 3 days of F@#%ing trying to mod here is how you can stop it from re-organizing as well as how to change mod load order super fast without having to click one arrow at a time.

First you need to be on PC of course. Then find

C:Users[NAME]AppDataLocalLowObsidian EntertainmentPillars of Eternity II
NAME is your user name on windows.

inside you will find modconfig.jsn.

You can open that file with a txt editor or even an updated wordpad (which has line numbers on it).

This displays your current load order and you will notice that at the bottom will be the steam mods.

Right click modconfig.jsn, go to properties, then click read-only in attributes. click apply, click okay.

Now when you load the game it won't automatically change the load order.

Now, you can go back to the file, change the txt in the file.

a mod is {modinfo}, and only the last mod is {modinfo} no coma.

change your order and save it, make sure to put it to read only. launch the game and go see your load order. if it hasn't updated click refresh. At this point if you don't have readonly on then it will reorganize your mods to default. if it is on then it will organize to the order you manually did.

ALSO you can edit the .jsn file while the game is open just make sure its on read-only before hitting on refresh in the in-game mod menu.

There you go, a quick way to edit your mod order AND make sure it stays in that order.

PS! MAKE SURE YOU RESTART YOUR GAME IF YOU DID CHANGE THE ORDER WHILE IN GAME!

Some mod stuff doesn't work unless the game is restarted.