If you ever used the desktop version you would know that there was a way to add the markup but not show it on an estimate or invoice.  I mark up all my materials.  It pays for my admin.  I currently can't use quickbooks for estimates because I can't use this as a feature.  It's a glaring omission.  I just can't figure out why they couldn't bring the same features over from the desktop version.  For as much money as everyone pays them, it's seriously messed up.