Hey Stephanie,
I want to first highlight that currently in Method you can start with an estimate, and convert that into a WO. Once that WO is complete, you are able to convert it into an invoice. To gain access to this feature, you must have Method Full Blown with Field Services imported.
Currently you cannot do this in QB, so the default Method screens will not allow you to do this. Now since we are talking about Method, yes, Method can be customized to allow your users to flip an invoice into a WO, Print a shipping ticket and a packing slip. There is a drawback, QB will not have any way of knowing that you have converted the invoice into a WO. When you customize the screen you will need to create a way to tell what has been converted and what has not been converted.
You will also need to use the Report Designer to create a shipping/packing slip, I'd suggest customizing the current invoice report and just remove some fields.
If you need help with customization, take a look at our webinars. If you get stuck just contact your business consultant to book some consulting time and we can help you get moving forward again.
Below is a link to the Webinar section of our website.
http://www.methodintegration.com/cs/blogs/methodblog/pages/Method-Community-Webinars.aspx