I never mark up materials or equipment rental. I bid my jobs with an estimate on what I expect the materials to cost, and a solid number of what my labor will cost. I decide what I want to make for the job, and if I have to take time to go rent something, haul it to the job, or have it delivered, and then deal with fueling it, cleaning it, loading it up again and returning it, that all factors in to what I charge in my labor.
In my opinion, clients are tired of being nickle and dimed. They like being able to budget a job, and they hate it when the contractor says they need more money once the job starts. If you bid the job low, suck it up with a smile, do the job to your very best ability, and learn from what you figured wrong.
I also always over bid my materials estimate by 20% on average so I come in under budget on every job. Last one was over $400 under what I bid it. They where VERY HAPPY!!!!!