Menu Builder Question

So I have disabled certain mods from showing on the main Menu display.

But what do I have to do to move menu positions around. Do I just move the first top box on the menu builder admin and position it where I wish? Will the rest of the items (boxes) below the main menu title follow it and position themselves underneath again where i place the top one?

correct you just move the top one  if you click on it or the green ones bellow you have the option to set who can see it

So once I move the top one, the rest follow wherever I resettle the top one again?

That's correct.