I have done my up in several batches. When I made some in a double boiler, I started getting separation right away. I lost patience as this was taking a lot of time, so I decided to speed up the process. When I put the pan right on the burner, the fat melted quicker, but it seemed to homogenize the final product, and it does not show much sign of separation after several weeks. I think that I may have cooked the oil out of it, and all I have left is the grease. Seems to me that the best way is to go with the double boiler and keep dipping out the oil as it forms.
BTW, make sure you strain any bits of meat out of it. I had to pitch a pint that stunk to high heaven, and I saw little bits of solid matter settled to the bottom of the jar. I think that is what spoiled and contaminated the whole jar.