When you create a sales order and then use that to push over a po/estimate/invoice, dtools will not let you push over the same info twice. Therefore, it makes it pretty difficult for you to invoice for the same item twice. For example, if you create a sales order for the rough-in phase, and then go into quicklinks and push over a po for only some items in that sales order, the next time you go into dtools and go to generate a po for the remaining items, you will only be able to push over a po for the remaining items in the sales order. You will only be able to see the items that haven't been pushed over. A nice safeguard so that you don't double order/bill.
On the other hand, if it's a large project, pushing over the entire sales order can create extra work for you if the project changes during its lifecycle.
Another option is to create the sales order for the necessary phase of the project as needed and use your contract percentages as guidelines. And begin submitting a 'Request for Payment'. This can be a document that you create in word that has your logo and other company information on it along with any other necessary information. The project that you have created provides you with a nice proposal report that can essentially replace an invoice (*only for the customer does this happen, in the sense that everything is spelled out for the customer in a detailed format and in a way that they can visualize the entire project from the proposal report). And if you go and create an invoice that you show to the customer that comes from QB from D-Tools, this can often be used as a shopping list since it has the model number and description and price nicely grouped together (depending on how you have your QB file set up of course).
Once you receive payment from the customer, then you can create an invoice/estimate in Quicklinks, transfer it over, and use that to receive the payment, monitor your inventory, etc. The customer doesn't ever see the invoice that is generated in QB, but they don't really need to if your proposal report is solid.
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