The payment system isn't confusing, is the ppl are confusing, is straight facts that;

*This is for the period of 6th Jan 2012 -> End of V1.XX.
1) Base Service (Only account no characters) : 6.99
2) Character : 3.00, any extra will be another 3.00.

You get 1 account (6.99) + 1 character (3.00) = 9.99, if you wish to get more character add extra 1 character (3.00).

Why they do this?
Because of the sole reason of having only 1 character to play all class/jobs, because of this systems, they implement this type of payment system, and to not cheat in a way, they lay out the payment details like above.

so for default 9.99 is actually " Account + 1 Character ".
But ofcourse for the duration of this 7th Umbral Era, you'll get 2 free retainers, anymore will be adding 1.00.