Well, the ideal is always to have no air. That being said, it is best to have the highest point in the loop be a res or fillport so that as the system runs, air bubbles can be pushed through and eventually end up in a spot where it is easy to see them and fill the empty space. I know with my latest build I had air bubbles coming up for almost a month.
One thing I would recommend is to have the pump running when you are topping off the loop. The reason for this is that fluid moving through the loop will press out more empty space, so when it stops (if there is an opening) it will raise the fluid level, making it seem like the loop is more full than it actually is.