Unclear. You need to provide screenshots and explain better. Perhaps it's inherent in your shot, perhaps you are doing something odd, but we realyl need to know more and have visual feedback.
You are over thinking this and most likely you are camera tracking too much of the shot.
First, you don't need to attach a new layer to the original. The camera is the only thing moving so if you have a good track you can drop a new 3D layer anywhere in space and it will be locked to the tracked shot because only the camera is moving.
The easiest way to add your 3D objects is to grab your first target and select create new text or solid and camera. Then move to the next point in your track where you want an object and select a new target and select add new Text or Solid or Null. Then just match the position of the next layer with your artwork.
I usually only track shots from the first frame where the 3D object must be inserted until it goes out of frame. If it's a long shot like you describe where something comes in and out of frame and then later on another 3D object needs to be added I just split the layer and track the two sections separately. Not only is the tracking much faster when you do this, but it's more accurate and changes are easier to do.
Hope this helps.