OK, I think I understand what you mean, but if so, I would change the terminology. It is not mark up it is an allowance for miscellaneous material that is not directly covered. That is still material cost. Mark up is profit and overhead. Even then, so much depends on what you directly include in your estimate. If we are talking at the end of a job, you have figured out every dollar you spent, and all of your workers have recorded every hour they spent directly, then you have to figure things like, do you have a warehouse person or does the foreman order material and have it delivered directly to the job. the answer will change the amount of markup. Do you have a truck allowance in the estimate. Do you "rent" your wire pulling equipment, or a lift if you have one, or is it just part of the job. Let's say you have a warehouse person, you charge Project manager time when he processes a change order, but don't include his time directly in your estimate or charge him to the job, same thing with the warehouse person. Then IMO if you didn't make 25% over your direct costs then you certainly lost money.