I'm using Mod Organizer to manage my mods and have no idea where to put the ini. I downloaded http://www.nexusmods.com/skyrim/mods/51038/? guy's pre-made ini just because I don't want any mistakes. Where should I put it?

You should be able to install that just like any other mod. If everything is set up right in MO (i.e. it runs SKSE correctly) then SKSE should find the configuration file.

So if it's just the .ini file, should I create a few new folders respectively called Data > SKSE > Plugins and place it there before I install the the .rar with MO?