As riders it is our job to help the horse travel in a balanced, comfortable way.
If we are unable to ride with an independent seat, it is unfair to expect the horse to relax and stretch his topline.
The raised head and neck you are getting is a hollowing if your horses topline. The most common reason for this is that the horse is protecting himself from having his back made uncomfortable.
A horses mouth is quite forgiving, but the back is not, therefore it is essential to never punish a horse in the back.
I strongly advise you to seek some lessons on the lunge, on a quiet horse. You need to be able to ride without reins and stirrups, move each limb and your head independently, turn your upper body left and right without effecting the position of your lower leg, etc.
In rising trot, you need to be thinking 'forward, down' rather than 'up, down'. If you rise too high or straight up, you will be left behind the movement and come clunking down on the horses back. Allow the horse to simply roll your hips forward and down with each stride. There should be barely any daylight under your seat.
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