Decent instructions with AoC (they have some mod set up instructions available).

Some mods might have some requirements of their placement. I am not familiar all the mods listed above. If you are just starting out, I would start with a few to make sure it all works fine then slow add more.

Savage Steel 2 goes above Savage Steel 1 (per mod author instructions)

I typically clump my mods in categories. Which is not a requirement.

Pippi
Building Pieces
Placeables (with Building Pieces)
Gear
EL Map Mods
Game Features / Customiizations / Admin mods
Server Transfer Mod
Map Mods (Savage Wilds, The Empire of Stygia, Sapphire Exiles, Isle of Men/Women, Ghost of the Cataclysm for example)
LBPR
Hotfix mods

Good luck. That is just what I do in my setup. Although I do have a couple of exceptions (one mod requirement and I guess I did by choice)