"I'm just confused on how to make sure we bill all costs to the project when not using the Add Item option."
Run your Reports. That is how you manage projects.
"Sometimes there are more costs than the estimate"
Run the report Estimates vs Actuals Detail for that one job. This is how you manage if there are overruns = you see that different in this report.
"and we want to make sure they are all included"
They don't get included in Progress Billing. Let's review:
If you sign a Quote, and that is All I am charging you, then I need to manage that there is no Overrun. Or, I give you a Quote, but we will charge from Actual Time & Costs, and you agreed to that Scope as Not a fixed bid, but as a sort of Plan or budget.
Or, Both: We progress invoice from the estimate. As we work, we discover there is a need for an expanded scope = change order, and you agree we sill simply charge Direct Time and Costs for the amount outside of the original estimate's Scope. That is a Separate Invoice. I progress invoice from the Estimate. I separately invoice using Add Time & Costs, for the "Additional Scope."
"and there seems no easy way to make sure you cover all your costs by billing by percent complete."
Because agreeing to a Progress Invoice from an Estimate or scope is sometimes referred to as "not to Exceed/ Not to Succeed." The point of using Progress Invoicing is to be good enough to project your Costs and manage the project and build in the Price to cover your own contingency factor.
This is why some business only use Direct Time at Hourly Rates & Costs, or Time & Costs plus Markup. Not everyone can Bid a job and then stay to the Bid or Estimate. That is part of Project management, not QB.
You can finish a job and come in more profitable than expected under Progress Invoicing. You can finish a job and see less profit than planned due to errors in the Estimate, do-overs, improper supervision of labor, and errors in contracts with suppliers of goods or services.
I had one architect ask me, "How much can I work on this job?" The answer was, up to what you Estimated it will take. If you do Twice the work, we just lost money.
