How can I control which part of the object the fire/smoke is emitted from so instead of it coming from the corners it is emitted from the top side like a normal log on fire.
You can assign the smoke and fire to come out of just a vertex group.
Select the vertices you want the fire and smoke to come out of, and create a vertex group and assign the vertices to it:
Then go to Smoke Flow advanced and use the vertex group to determine where the fire and smoke will come out of.
Note: Every time you make any changes to the smoke/fire simulation you need to press Alt+A to update the simulation cache.
To set up the materials and actually render your smoke in cycles watch