The way Resolume works is that the layer controls are sort of a shortcut for the clip controls.
Everything you set up in a layer will affect all clips in it. Using the layer controls is probably the way you want to run most of your shows (if you work with more than two clips).
Sometimes there is a particular clip that needs to be finetuned, and then you can use the clip controls. All transformations will be merged with the layer controls and then rendered in one pass.
The idea is that you for instance scale down all your clips to 50% on the layer, and then have one clip that requires it scaled up to 200% on the clip. This particular clip will then render at its normal resolution, without loss of quality.
For more info on masking and transforms, I suggest checking out the masking chapter of the manual, particularly the paragraph on the render order: http://resolume.com/manual/en/r4/masks#render_order