Since i use an E3D v6 alongside my Merlins for comparison reasons i decided to put a silicone cover over the heater as well. It served me very well on the Merlin.
The design is simpler and has only two parts.
Just fill the silicone in the outer mold and gently press the inner part into the outer until it sits firmly. Silicone will ooze out at the rim.
Even if you use separation agents, chances are high that you need to destroy the outer mold part to extract the cover.