Yes you can have more then 1 active ffxiv account on a SE account.
each FFxiv account requires its own registration code found either in PC, PS3 or digital version.
Although you only need 1 copy of the game installed each copy only comes with one code with that 1 code depending on what lv of service you buy you can make
multiple chars for that 1 FFxiv account but they can not be logged in at the same time.
So to log in with 2 chars at once you must have 2 registered FFxiv accounts they can both be on the same SE account or on seperate ones it doesn't mater
SE is only saving you the issue of having 2 different logins is all.

Also about dual boxing on the pc yes you can run 2 instances at once as long as there 2 different FFxiv accounts once one is open just open another instance and sign in
if on same SE account it asks on log in what one you want to log in.

So to sum it up yes you must buy the game for each FFxiv account you want open at the same time.