Mod Instalation Order
 

Are there a mod/patch instalation order as I remember there was in SHII?

Use the JSGME utlity to install mods. It will warn you when one mod attempts to overlay another mod's file.

When that occurs and you're not sure how to proceed, come back here and ask, with the specific details of which mod is overriding which other mod.

As far as official patches, search The Community Manual for "update patches" for everything there is to know about them and mod's effects on them.