Jaymi, if you have your calculated shipping set up correctly you should not have to be giving refunds for $16.00, nor $3 to $6.
I've used CS since it was in prototype and I've only refunded 2 times. Once in this shop and once in my other shop. One time due to an item I had a flat rate shipping and a CS item combined, was able to get both in the FRE. Second time instead of sending regular Priority, I sent medium flat rate box PM.
If you're having $16 overages something is not set up correctly in your shop.
Either you don't have boxes to fit multiple items in or your putting the box size for the item size and CS is figuring an even bigger box or you have handling fees that are being added per item and per order.
Dimensions:
Item + any packing, NO box.
If you fold an item to mail, you use that measurement.
Weight:
Everything, item + packing + box.
Handling fee:
On a shipping profile, fee is added PER item.
On a box in package preferences, fee is added PER order.
If in both place BOTH are added to an order.
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I would not send a check to anyone for a refund for shipping overages.
You have NO proof you sent it if a claim was filed on that item.
If I bought something I would NOT like getting a check from seller for a refund, I'd expect to be refunded through how I paid.
I'd refund through how they paid either Paypal or Direct Checkout.
If the buyer ever opened a case on you for item not received or not described Paypal and DC would both refund the buyer the total amount of purchase paid. You'd be out that money you sent as a check for a refund.