When the payment comes into your bank account you will simply drag the invoice on top of the payment and label it a Partial payment. The invoice will automatically get updated and you can send your customer an updated documents. 

For example, let's say you invoiced Acme inc. $1,000 for your SEO services. They paid you $500 and that payment is now in your bank account. 

When you go to reconcile your bank account you'll see $500 in the left column and a $1,000 invoice on the right. 

Drag the $1,000 invoice to the left and you'll see these options:

Select Partial payment.

Then check out your invoice. It will now show that partial payment. 

From there, you can send your customer an updated invoice. 

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