Look its really simple you should sit down and think for a moment. Draw on paper or whatever works for you.
This is computer technology form early 1970's btw, just because you dont see the inner workings day to day- I mean the foundations put in place in the beginning will affect your life every day use for the computer. Compueter use dont get much more fundamental than this, this is the basis for almost everything the computer does.
Think of how you work in real world:
If you need a screwdriver, you go and search the screwdriver form the toolbox, if you dont find i there you go and look for it on in the garage first on tables and floors.... when you find it, you stop searching. Even if you had 20 screwdrivers you search only for one thet fills the description and terminate after this.
now what the hell is the env file? Its just the list of things that you can search for, and instructions on how to search for them. (so its a lists of items which are a list of places to look for screwdrivers).
EXTRA course:
To complicate this a bit further its actually chained. Theres not just one ENV file theres many. They get appended to each other. (why is there many places you can set things, well lets suppose you are a computer operator in system that manages the entire telephone system chain of the world, its impossible for you to manage it all by yourself, however you don't have to you just manage one region and let others manage whats outside o this). So the env file is most likely pace to find something.
NOW its really really important that you know where the FIRST instance of said file in the list is if theres 2 of them only one EVER gets called unless you implicitly call both with full pathnames.
However you can ask maya wich file is the one it reads by asking it.
whatIs userSetup.mel;
and maya will tell you:
C:/some/folder/with/scripts/userSetup.mel
NOW userSetup.mel is jut one file that gets always called when you start up this is whre you should put all your customizations.
NOW the mlls arent autodoaded, they are autoloaded becaus etheres a mel file that does it.
Again when maya gets started only one mel file gets loaded! however this mel file calls all the other files. INcidenttaly this file also loads a file taht autolads the plugins too.
One of the last things it does is calls userStup.mel so taht you can make yoru own customisations
PS. you will bash heads forever if you dont exactly understand how this works. Especially if you dont know how the OS environment works because you will need it if you ever do anything more involved