So you ran out of heating oil and you have replenished the tank. Now the stupid burner just runs for a while and then the reset kicks it back off. You have fuel and still no heat. The problem is probably air in the pump. Here is how to correct that problem.
When you run a burner oil pump out of fuel you get air in the pump. The fuel pump is a gear pump which makes pressure by running a couple of gears together pushing oil through at high pressures. Anyway because of it being this type of pump it has a hard time getting air moved out and sucking oil in. If the air is not bled out of the pump at he proper place it will not prime.
To find the pump, you need to look on the right hand side of your burner. The pump is the black box like thing that is about a three inch cube. On the bottom right of that black cube is a small nipple that protrudes out about "". A small wrench will turn that nipple open. Counter clockwise is open. and wait for the air to bleed from the pump while the burner motor is running. it will just suck air back in again. This is especially true if the burner is higher than the tank.
Once you get a steady stream of oil out of the bleeder valve, close the valve and the burner should fire. If you may have other issues. It is not uncommon to plug your filter or nozzle when you run a burner out of oil. Running all the oil of the bottom of your tank will often pull some sludge into the system and cause more problems.
A couple of other ways to avoid having to bleed you burner is to either have the pump piped with two pipes or to install a TigerLoop air eliminator. If you have either of these setups you probably can just push the reset button and the burner will purge the air its self.
Be patient, it may take a few tries to get the hang of boring your burner. There is a bit of a trick to it that you will figure out quickly. You now have the basic steps and it is not hard to get the rest down easily.