There is no incorrect way to use the orders, if you set a limit buy above the market price, then bitcoinica says to itsself 'oh shit guys we're already below that price... execute now'. if you set a stop buy (weather or not you have a position open) below the market price then bitcoinica says to itsself 'oh shit we're already above that price... execute now'.

I think there may be a fundamental misunderstanding of how the orders work,
Basically:

Limit: makes you money by executing your order when the price reaches a point in the profit direction.

Stop: cuts your losses by executing your order when the price reaches a point in the loss direction.

trailing stop: cuts your losses by a set amount(of loss), rather then at a set price.

And any of these orders can be used to open, close, increase or partially close a position.