there isn't anything that would need figuring out - you just download all the mods you want, run the manager, load them all up into your SS2 install, activate them and arrange the priorities according to the picture (in the guide I've linked), using the increase/decrease priority buttons. this is needed for everything to display correctly, but won't break the game even if you get it wrong - you just won't get proper hires models everywhere, for example.
the tool modifies the game folder structure, so the game may appear broken or missing to steam or galaxy. this doesn't really matter, but if it bothers you, you can always keep the steam/galaxy build intact, and just copy it someplace else, and patch and mod the copy, so steam/galaxy won't complain.
mod loading did change in recent years - because now we finally have tools that are safe and easy to use. also, most mods have received updates that make them incompatible with the old ways of mod loading, so not using the mod manager is strongly discouraged.
Post edited September 30, 2016 by voodoo47