How do you get subcontractor/vendor costs to be included in the contract amount on a phased joint invoice? When running invoices, you do not want them to show up as expenses beyond the contract amount.
If expenses are included in your contract amount, then make sure to apply the project rule 'Include billable expenses in the contract amount'. If any expense has already been entered in your system, then reverse or delete that invoice and uncheck the Extra flag on the expense entry. When you reprocess the invoice, it will be included in the contract amount.
In general, when entering expenses, you can use the Extra flag to identify the expenses that are part of the contract and those which are over and above (i.e., Extra) that.