Add a layer of soil mix to hold the cover you choose over the holes. The goal is to have the newly repotted plant sit in the new container at the same level it was in the old container. Place the plant in the pot. If the plant is too deep in its pot, gently and slowly lift the plant and allow some of the soil mix to fill in around the soil ball. If the plant sits too high in the pot, you'll have to lift the plant out, dig some soil out, or just dump the pot out and start over.
Some folks like to put stuff like gravel or charcoal in the bottom of their pots.
The plant will be better off without it since more of a good soil mix will be available for the roots to grow into. Stuffers like to press in the soil around a newly potted plant. Fillers like the plant to fill the pot to the rim and let the soil settle in with the first few waterings. Most people just seem to be one or the other. I happen to be a filler most of the time.