This shouldn't be too hard for all you veterans out there :)
Basically I've used the motion tracker to stabilise some footage, and applied it the the video layer. But now I need to move the layer around the comp, but whenever I do, it edits the keyframes set down by the motion tracker.
So how do I stop Ae from editing the keyframes once they are set!?
Do you want to move the layer to a new position, or do you want to animate it's movement?
For a new position, click on the 'position' property to highlight all keyframes, then simply click and drag.
To animate, create a new null object and parent the layer to it. You can then apply transformations/keyframe position of the null object, and the motion tracked layer will follow it.
If you want the layer to actively move around.
You can create a null object, parent your layer to this null and then move/keyframe the null around to get the movement you want.
If you want the layer to stay in place but at a different position
Select ALL of the keyframes of the property that you want to change (Click on the property name).
Make sure the timeline marker is on top of one of the selected keyframes.
Move the layer.
You could also precomp the layer and then move the precomp, but first you would have to solve scaling and clipping issues caused by the stabilizing.