Unfortunately the Invoices feature on Square needs attention all around. As far as I know they would have to pay it from the invoice on their own, not at the POS. But beware, once they do, paying the balance is another long standing problem with the invoices. The balance can't be paid over the POS but you have to send them a link (not a new revised invoice as you might expect) to pay the balance which they have to do on their phone even if they are right in front of you with a credit card. You will then have to go to the virtual terminal to mark it paid by Square as there is no option on the POS.
There is no good work around. The only thing I can suggest is to take the payment separate from the invoice for the deposit and write the invoice for the balance due amount. Basically, two unconnected transaction. You can always do a paper invoice showing all the details (total amount, deposit paid, etc.). Not ideal but frankly Square is very slow moving in addressing the various invoice issues. I use the feature daily but I usually do not need deposits and if I do I invoice for the remainder once the work or sale is done.
We definitely don't have a perfect solution for this variation in Invoices at this time, but it's something we're continuing to iterate to our Product Team.
The best solution we've encountered for people in situations like yours are a "Deposit Invoice" and a "Balance Invoice." You can create these by using the Recurring Invoice Option.
When you do this, you can mark the first Invoice generated the Deposit amount, then mark it paid from the Point of Sale. Your balance due invoice will then send when from your Dashboard automatically and allow your customer to pay the invoice online. Recurring invoices are also editable, so you are able to change the amount due after you've set up the recurring payment.
When you have created the first invoice (the deposit invoice) you can then mark it Paid from the Point of Sale. This will show that your customer has made a payment in that recurring series.
If you need to make changes to the balance due email that is generated, just click on it, click edit, make any changes, and hit the Update button. This will allow you to take that payment as an credit payment or you can also mark that one as Paid in the Point of Sale, if they should choose to come in and pay it.
We're aware that this is not the most ideal work around, but it allows you to be able to take payments in both ways and organizes the invoices in a way that will allow you to see recurring series on your customers. You can even break the payments down further if needed.
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