There's no right or wrong way to use the plugs and caps. In most cases, the placement of either is interchangeable and based off preference. From off our experience, we like to recommend the below. 

Caps are great for; bong bases (where the glycerin coil goes) and both ends of the glycerin coil. 

Plugs are great for; Downstems and smaller glycerin coils found on the Bubbler and Bubbler XL. 

How to: Cover all holes and insert cleaning solution. Tilt glycerin coil / base back and forth so the solution runs through both ends of the coil or percolators. Let sit for 10 minutes. Tilt unit back and forth again and rinse thoroughly with warm water. Let piece dry fully before putting back into the freezer.