Ok answering some questions in a polite manner as told to by my OFPEC parole officer.
The Init.sqs is just like any other script except that it is automatically called before the mission. You do not need to call in, it does it itself. Much like the init field of a unit, these changes happen before the mission starts, before the briefing shows.
All you need do to make an init.sqs is make a new text file in your flashpoint mission folder and type whatever commands you want in it. If you really want, you could take all the init commands youve put into the units and put them in this sqs (though you would need to use names and not "this").
Triggers on the other hand, are not activated until the mission has started. Infact it takes them a few tenths of a second before they are activated. Which is why you might see a flash of your character before a trigger activated intro.
So there you have it, init.sqs good, triggers bad. Init fields are exactly the same (but without a script and not very well organized).