We have the same situation. Unfortunately we have not found an easy way to do this either. The one thing I did do was set up the description of the contract items with ** in front of the description to easily see which ones are Allowances in the Contract and the WIP. After you "fill "your allowance costs you can make the status of that cost code Complete and further postings will get a warning message. We then set up change orders for the overages, usually more than one. For instance, CO#01-Dumpsters & Carting 1, CO#01A-Dumpsters and Carting-2 etc. 

Thanks for the reply and recommendation.  Sounds like a good workaround for now.

Aaron, I would love to talk to you more about your needs here.  I have a couple of ideas, but need to ask a few more questions.  my email is [email protected].  Drop me a note with where you are located and we can schedule a time to talk.  I am in Dallas this week, Portland next.