I always cut a cross + in the cover, and just separate the parts and plant the seedling in there. When they are much larger, I simply cut the cross larger, though sometimes, it gets sort of difficult. Last season, i had to keep some peppers indoors much longer than normal (and re-pot them again!), due to cold, and had pots with over 3 cups of mix in them, so I removed some of the mix in the EB, and set the plants in the holes, and packed it around them. For small rootballs, I don't bother with this.