Hi E.,
We loved our Amby bed - our 22 month is too big for it now - but he slept beautifully in it for 13 months.
The first thing I would suggest is not to put your baby to bed asleep. It's not terribly surprising that he wakes up when he leaves the warmth of his mommy's arms and hits the cold sheets. Put him in bed awake but sleepy and let the rocking of the bed lull him to sleep. He may cry a bit at first and he may need you to bounce the bed a bit to get it going, but this will not only help him get used to his environment, it will also help in the long run because if he learns to fall asleep on his own then when he wakes in the night he will know how to put himself back to sleep without you.
As far as the head being lower, I don't think it's unusual for it to be a tiny bit lower. If it's too low then try putting his head at the other end of the bed and see if it makes a difference. Also, try moving him up higher in the bed. That may help.
Good luck. I am sure you will find the right balance. All the best, D.