I will be using a webstore which brings over sales orders to NetSuite. Is there any easy way or best practice to have these sales orders go to an invoice that then becomes paid rather than going directly to a sales order / cash sale? I'm not sure if the invoice should have a customer deposit which is then automatically applied, or just have a payment generated after the fact. Anyone else dealt with skipping a cash sale and using invoices for ALL transactions?

Yes. Invoice then Payment created