I don't know of any product that would do this but have you considered creating a location for each customer say equal to their customer number.  Then you could get the driver to create a transfer between the truck location and the customer location.  This could even be a spreadsheet and then you know exactly what each customer has taken.  This data could then be used to create a sales order directly into QAD.

So for each customer we may have hundreds or thousands of ship-to locations.  That's part of the problem, is that creating an invoice from scratch for each location drop off is way too much work.  
Right now I'm boiling the process down to this:

1.  Yard manager creates delivery list for driver in excel in the order of delivery.

2.  Product is transferred from yard location to truck location

3.  Driver fills in quantities on printed out excel spreadsheet as they drive around making deliveries.

4.  At the end of the day the quantity in the spreadsheet is audited against what is returning in the truck.

5.  The unused inventory on the truck is transferred back to the yard location

6.  The spreadsheet is updated and sent to the home office to create invoices for each site delivered to, this relieves the inventory from the truck.

Overall, it's pretty clunky.  I'm going to have to do something to make it easier to generate pending invoices off of all of these deliveries, or hire a lot of data entry clerks which is not a good plan.

Even though you have multiple ship-to's for the customers I assume you would just invoice one big order?  If that is the case then you would only need one location per customer.  The reson for doing this is that depending upon the version of QAD you have you can define a location to be specific to a customer, so once it is transferred into that location it cannot be sold to someone else.  So if you say set up one spreadsheet for each customer regardless of the number of ship-to's and the driver kept that upto date with what he "sold" to each delivery point.  Then when back at the office you could use the excel sheet to create a CIM to do the transfer to the "customer" location.  then maybe once a week you could again use an export from QAD by location into a spreadsheet and use that to create a CIm to create an invoice for everything that is in that location.

This would allow you to have multiple receipts(drop offs) per customer per day/week but still only create one large invoice say once a week.  And the location contol could be set to non MRP so that MRP would know about usage even before the invoice had taken place.

Still clunky but would not require any extra staff

No, unfortunately every single ship to has to be a different invoice as dictated by our customers :).

I'm thinking about trying to use excellerator to create sales orders from the delivery sheet our yard managers fill out for the drivers.

My approach would be to sepparate all mentioned topics and solve them "independantly".

For instance the QAD sales order -legal- creation and the QAD "goods shipped" information can be handled independently.

On the other hand you have the Real inventory and the QAD (model) inventory.

First you might consider using Customer schedules were you can setup all customer/ship to condition in advance.

Second: reporting of delivered goods is now much simpler, you only have to ship to goods from your truck location to the customer and you are finished.

Third. "Real Time" logistic reporting. If this is important you might consider a "mobile" terminal. With this mobile terminal you can login anywhere and you can record "Real Time" goods shipments thus triggering Real time inventory transactions and, optional, immediate invoice creation. (Simular to a DHL delivery truck.)

So depending on the importance of this issue (=bduget) there are solutions.