When you pollinate, the words to live by are:

Less is more.

Keep your pollen in a small envelope or vial and apply it with a Q-tip to a plant that has been removed from the flower room. Label the branch. Where on the plant you pollinate makes no difference as to what your results will be; I do the low buds so as not to seed up the valuable top colas. You may use pollen from more than one male and make several different crosses on the same plant, but be wary as crispi noted that pollen gets EVERYWHERE in even the slightest puff of breeze. Let your pollinated plant sit by herself for a day or so, then mist her to deactivate any remaining pollen and return her to the flower room.