You can do it, if you invoice your customer for all projects at the same time. create the invoice for the customer through the customer list and not through the project itself. you will be able to add all your billable expenses thought that. it will separate both projects with subtotals, name them (the name you gave the project). But WARNING DO NOT GROUP TIME. For whatever reason when you group time by services it does not split the time appropriately per project. it will not split a time service, therefore it will appropriate a complete time service to only one project even though you have some in multiple.

Other than that, yup, creating your own boxes to fill out every time is the only way to do it. I agree, there seems to be lots of things that need worked out.