Air will rise so having the res above everything else will help, if this means giving the rig a slight tilt then so be it. I usually fill the res not much more than over the outlet, turn on, let it drain a bit, turn off then repeat till full. Sometimes i'll let it run for a minute or two between top ups towards the end which seems to help. Over time (few hours) you should get most, if not all of the air out leaving the res cap off.
I'd agree with not using the 'pea' method. I tend to go for a cross, apply pressure on the block, lift to check spread then re-apply if needed and job done.
How have you got your fans mounted and what speed are they running at?