QBO recording credit card discounts on customer payments

We moved from QB desktop to QBO and I'm finding doing receipts for customer invoices through Square or Shopify a bit odd - I've found a couple of options but they seem to be more of a workaround than a regular process.  Maybe there's another way I'm not aware of.   Shopify bills in US then converted to CDN so you don't know the discount until it hits the bank.  

The 2 workarounds that have been suggested:

1.  Go back into the invoice, add the credit card discount as a line item and resave when doing the deposit.

2.  In retrieving the bank transactions, it shows the net amount, so won't 'match' to anything.  So, go and find the invoice that is being paid, enter the full amount as payment, then fix it by entering the credit card expense.  

The other glitch I am finding is that the QBO bank rec numbers for deposits and payments do not line up with the bank as the deposits are overstated and the payments are understated by the amount of credit card charges for the month.  I would use those totals on the QB desktop as a verification step when reconciling.

Again, I am hoping I am missing something.   Accepting credit card payments is a big part of our business and I am finding that and these solutions aren't ideal.

Thanks in advance.