Yes, you should remove any areas of cloth that aren't adhered to the hull. If they are small (5p piece or thereabouts), just fill the space to level the hull surface. If significantly bigger, lay in another piece of glass cloth and sand the edges flush when dry.
Ezecote doesn't respond well to the credit card squeegee technique, which is really aimed at epoxy coating. Ezecote is too thin to be smoothed across the glass cloth but I suggest using a roller. I use a roller for epoxy coating, as it gives an even distribution, presses the cloth into contact with the wood and is much more economical with the epoxy (which isn't cheap!) than the "pour it on and squeegee off" technique. Ezecote is a lot cheaper, but you still want a nice even coating that saturates the cloth. Rollers are the way to go IMHO.
Greg