I leave the funnel in there the whole time.I don't get it yet, when you use the pen grip as the mouth piece are you just pulling out the funnel?
I have it so it is sitting just above the bridge of the atomizer.
The best way to position it so it is sitting just above the atomizer bridge is to put the pen grip on where you want it to sit, then push the funnel down until it stops going further because it is touching the bridge, then back it out a little bit with tweezers.
The trick is to cut the pipette in just the right places.
I like to have my funnels be flush with the top of my pen grip, and as wide as possible while still being able to push them in with some effort and so they are a little hard to pull out even with tweezers, thus assuring a tight fit. That way once you have them where you want them they aren't going to move.
You also want to make sure to use the straightest pipettes you have.
I toss any that aren't perfectly straight.