I have found Priority Mail shoebox size and the #7 size the most useful for shipping daylily orders.
I've had to readjust what I charge through the years (and after taking a few painful hits with sending things to the west coast for too little postage.) Though it's not stated in the shipping information, I'm usually going to include something extra. Here is what I say about shipping in my catalog.
Shipping is by USPS Priority Mail.
East of the Mississippi: $13 for the first DF or TF plant ordered and $2 for each additional plant in the same shipment.
West of the Mississippi: $15 for the first DF or TF plant and $3 for each additional plant ordered.
Add $1 for each CLUMP.
This seems to work out pretty well for both side as far as I've been able to tell.
I agree that the flat rate boxes are not a good deal unless you are shipping lead weights.