If someone is assigned first pick, does that mean that if both players were to pick the same 3 areas in order that person would get all 3? Or would it alternate as the first and the third (Fifth, seventh etc..)?

No, it actually doesn't work that way. I wondered that myself, for a while. There's a good explanation on the help page: http://warlight.net/ViewHelp.aspx?s=Distribution

Basically, you would get your second and third picks, even if your opponent chose the same exact starting spots.

not correct crafty.. if you and your opponent chose the same exact 6 spots, then first pick would give you 1 4 5

it goes abbaab

and i misread what you said.. yeah, you would get 2-3 if your opponent received first pick