Which kind of bead tip are you using? There are the "cup" type, with a hole in the cup to thread through, and the "clamshell" type where the thread passes through a hole in the joint of the clamshell. I find the clamshells a lot easier to use. Also, precious metal ones (gold, goldfill, or sterling silver) are a LOT more sturdy than the base metal ones. They'll rarely line up exactly, but one way to "smooth" them (sort of) is to squeeze a tiny dab of cement (I use Hypotube) inside. That secures your knot and holds the whole thing together.
For making the clasp connection, use the tip of your round-nose pliers. I grasp the very edge of the tongue and twist in a curling motion, to tuck the very tip inside and make an overlap. Another dab of cement can't hurt, just wipe it clean.
Hope this helps!
-- KarenK Desert Dreamer Designs