You have to submerge the whole nib, which will leave part of the assembly looking like a dipstick. Of course, you then have to wipe the ink off the dipstick. (At least it will help you know when it's time to buy more ink.

)
Couple of hints:
(1) "Creepy" inks like Noodler's bulletproofs crawl on the metallic surfaces and sometimes into the internal mechanics of VPs. Since the stuff only creeps on metal, "waxing" the "dipstick" part of the assembly creates a creep barrier and will keep the insides free from ink.
(2) While you should be able to see the ink in the converter, the twisty converters won't fill ALL the way, and since the converter is small to begin with, many people (me included) want to fill the things all the way up. After filling the ink, point the nib upward and give it a few flicks of the fingernail, the way junkies in the movies do before shooting up. Then twist the air out, then resubmerge the nib and twist ink in. Then the best thing is to twist 3 drops of ink out, and then twist air back in. This leaves some air, but just a little -- enough to keep the full converter from burping up little blobs of blue onto your clean sheet of paper.
Hope this helps. I really love my VPs -- hope you do too!
Doug