I have a base GPUImagePicture (Layer 1) and then another GPUImagePicture (Layer 2) that I have added a bunch of filters to.
When I put them together into one image they look fine but what I would like to do is move Layer 2 with my finger to different positions on Layer 1. Is this possible without using something like Cocos2D?
Try to add an GPUImageTransformFilter with an affine transform set correctly to translation to one of your GPUImagePicture before blending.
If you need to make a more sophisticated manipulation I think that you should extract from one of the original image the correct portion, redraw in a transparent background image (same size of the first one) and then blend.
To build the affine transform to apply you can easily use a UIPanGestureRecognizer on a touch detecting overlay view.