"Tips & Tutorials - if we place an order & use our debit card, when we receive the order I will use the "write checks" to enter the transaction (no PO or bill is entered)."
That;s fine; the issue is, if you need to be able to access Items or not.
"Even if I use the write checks it adds the inventory."
Because you listed Items, and did not post to accounts. The Deposit screen only provides for Accounts. A Vendor Credit provides for Items, and then a refund would be AP.
Or, a refund is just Make Deposit, as "from" COGS or Freight expense.
"That is correct that I enter the shipping expense as COGS-Freight In and then I used that same account when entering the deposit for the refund on shipping."
You are being told that inbound freight is supposed to be Costed into the products you got. Ask your own CPA about this. Example: You buy $5,000 equipment with $500 shipping inbound = $5,500 Basis.