I had to rething your post a few times to understand.
do u have to put a clip in a new layer everytime of can u put the clip 'ontop' of the other one?
If I guess/think right you mean everytime you want to overlay it with a clip, you have to put the clip over the other in the timeline? Uhm... in general yes of course.
im not sure but i think when i did that it cut the clip it went ontop of
You´re working with what program? If you work with AE and "cut" (in AE it is splitting a layer and not cut), it wents up into another layer. In Premiere: no it stays in the same timeline.
After Effects works in that way that, it always makes a singel layer for a clip (you can´t put two clips onto one layer in AE; that´s why you split and not cut).