This term most often refers to placing a single piece of glass over the whole of the project. The decisions relate to whether to do it at all, in what circumstances and in what order. Whatever you place on top of the project is what the eye will first see. A tinted top layer will give that tint to all the pieces making up the object. So most often the top is a piece of clear glass.
Many times the purpose of capping is to give the volume of glass required to keep the piece contracting as a result of the surface tension of the glass trying to pull itself up to 6mm thickness.
When using opalescent glass as the main component in the work, you should consider capping with clear. Opalescent glass is slightly more prone to devitrification than transparent glasses, so any work to be fired a number of times might be best fired with a clear cap. It also protects against any bubble formed between the other glass and the cap showing as a clear spot within the opalescent as it pushes the colour aside and reveals the clear below.
There are some times when you should consider placing the clear on the bottom. If your design layer is made up of lots of pieces where air might be trapped, but is uneven enough to be the likely cause of bubbles, then the clear should go on the bottom to ensure there is sufficient volume. An alternative is to do a high tack or full fuse of the whole upside down on fibre paper, then clean up and fire right side up with the capping glass.