Definitely the best way is to have the granny flat as a separate zone. You will only require one pump as long the main part of the house is zoned also and when heat is called for in the granny flat, it does not heat the main house and the pump is sized correctly to be able to pump both dwellings at the same time, otherwise a second pump will be required. Also ensure that the boiler can handle the extra capacity too.
With regard to oil tanks, this is more complicated and certain regulations will have to be met. For example, a bunded tank must be used as it is supplying a property other than a single family dwelling. It will also be more difficult to separate which oil tank is being used. For example, when both dwellings are calling heat heat at the same time, which tank will be supplying the one boiler?