Hi there, I feel your pain regarding the flying through boxes test. I originally applied for the easyJet MPL in June, sat Day 1 and on this test I got 4 4 5 (out of 10). I failed the PILAPT.
Ultimately, you must get a flight simulator - personally I love x-plane - the aircraft you fly roll and therefore bank. No aptitude software currently does this so unless you fly on a sim it'll seem alien to you. Just practice manual flying with gentle movements and remember when you turn left you need to stop the roll by counteracting (turning right). To make it harder try this for an external view of the aircraft - this really works well!
For skytest, as people have mentioned, alter the settings so that you are flying through boxes. Make the boxes as small as possible. Add a small lag so that you know what to expect. Make the run time slow, it's not that fast and what ever you do you must have small, smooth, calm movements otherwise you'll get nowhere. Finally just aim for the centre of the square, do this by only looking at the one closest to you.
I took my resit of the PILAPT in september and this time round I got 8 8 9. I'm now through to stage 3 and have it in November. Best of luck with your preparation! There's a virgin MPL chap who failed numerous times before, but look at him now... he's certainly not complaining
