Hi Missy. It's always best to check with the seller before assuming anything. Every seller can have their own way of doing it. When you look at a daylily on the LA, there is a link you can click to "contact the seller". So I would ask.
However, I have done exactly what you described in previous years. Order some, pay for them with the delivery amount. Then when I ordered more, I just had to add the +$2 per plant when I ordered more later. When the plant count got high, checked back in to make sure we didn't have to worry about how to handle if I ordered two boxes worth of plants.