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To all those who mark up material,do you then have to do sales tax? My accountant thinks I do if I am reselling material at a higher cost then I paid for it.

This is probably a state by state issue. In my state if you break out materials and labor and charge more than you paid for the material, you should collect the additional sales tax for the state. They don't enforce this with small service companies, however we avoid this by selling the job as a fixed price for materials and labor. We mark up the materials when estimating, we just don't list it out that way.