Just to make sure (going back to basics here so don't hate if you are beyond this)
Once you remove your cooler to add a new layer, I want you to properly clean your cpu off and the bottom of your cooler, they should be as clean as possible and no traces of the previous applications should remain.
When applying a new layer of paste, a small amount goes a long way, I quite often see build that have had far too much applied.
Pretty simple stuff.