Well, technically they would be paying via card twice on a single invoice.

Once for the deposit, then again for the final payment.

So the question remains, are the fees assessed per transaction or per the whole of the invoice?

Sorry, I didn't completely understand the question.  Square will only take fees out of the amount that's paid, not the entire balance.  So if your customer pays $20 of a $100 invoice via credit/debit, Square takes their cut out of the $20.  If the customer then pays the balance via cash or check, Square will take no more fees.

I hope this answers your question completely.

No, it doesn't but thank you for trying.

There is no cash or check involved in this scenario.

Let's say I send an invoice for $100 and request a 20% deposit.

My customer pays $20 for that deposit.

A month later the rest of the invoice is due.

My customer pays $80 for the remaining balance.

Two (card) transactions. One invoice.

I assume the fees would be as follows.

$20: 2.9% + 30 cents = $0.88

$80: 2.9% + 30 cents = $2.62

Total fees: $3.50

Had it been a single transaction for $100 the fees would have been $3.20.

In a nutshell, I'm trying to figure out if the use of the deposit feature is going to cost me 30 cents on every invoice.