You need to use the toggle hold weights option once you get the area weighted properly. Also work from the hands to the shoulder then work on the head to the neck then the legs to the bum then finally the chest and abdomen.
I always find this process a nightmare and found the setup machine to be very usefuly as it does the weighting for you. You will still need to tweak the weights once it had done its thing but it is a massive help. Since using it I have been able to get a character done to a decent standard in around 2 hrs + it creates all the joints and curves so it saves a massive amount of time.
Hope this helps