What I do when we have "Additional Work" if we don't have the costs upfront  (mainly when doing rot repair) is use a cost code for that AWA work to post the costs and labor.   We have a Cost Code called "Billable" in our Cost Code List for any additional work requested if we do not have a CO in place.  Then I post to the billable cost code all material and labor for that work, calculate (w/labor rates) and either add the AWA to the Progress Billing or if you want to make a CO than you would have to go to each job cost and change the cost code to the appropriate one you put the budget to for the CO.  There are times we do a few other jobs they asked for so to track each one I use cost code 2801, 2802,2803...and this way you can calculate the costs per cost code (work performed).  Doing this keeps all the cost in the same job so no need to add another job for the additional work.  Hopefully that made sense to you!