Tracking all work/items-delivered are invoiced

We are a small business and use Xero.com (which is an accounting system without ERP functionality).

What we have found that we have at times lost track of items requested by the customer, and have found a couple of occasions where equipment/services delivered have not been invoiced.

We have forms for Invoice, Delivery Note, and sometimes (not always) a client purchase order as a reference.

We do not have any paper structure that ties this together, so what would be the best way to have a ledger/form to include in our business processes that will drastically reduce the chance of things being given for free?

I assume you're talking about B2B (business-to-business sales).

For B2B sales, you should always have Purchase Orders, which are issued by the customer. You do not process an order and create an invoice (or ship merchandise) until you have the customer purchase order in hand. I would recommend also instituting a basic checklist to make sure that the purchase order is valid, that the customer credit is good, etc. Then all you need is a filing system for these purchase orders; it can be as simple as paper folders sorted alphabetically by customer, or a simple online folder if you have the purchase orders scanned in.