Hopped is always added at the end of a boil. If the directions say to add the booster and LME pre-boil, then do so, but do not add the HME at the boil, it will end up too bitter.
Most Mr. Beer kits have you bring the water up to a boil, turn off heat, add the ingredients, stir, and then add to keg. Is it the same for that one? I would suggest using a whisk to stir everything vigorously in order to introduce as much oxygen to your beer as you can for healthy fermentation. Remember, the more fermentables you have, the higher your krausen can get.
What are the directions on the kit? That would give me something to work with.