in the large bottle i've been carrying for years (this bottle is smaller round than a quarter and almost 3 inches tall) you simply fill with water, wait until it saturates (and can be left sitting saturating ad infinitum), take off the top, pour the fluid into the cap, then dump the capful into the nalgene or milk bag.....
the crystals are heavy and on the bottom so i've never come close to getting them even into the cap.
Polar Pur (the product) has a filter built into the top just for this but i'm betting you could use a bit of cloth if you were unsure.
My next step once I get my hands on the iodine crystals is to see how much the tiny lid off the nitroglycerin tabs compares to the one on the old bottle i've got--ration wise that is.

One thing i've noticed over the years is that the glass bottle full of this iodine solution will stain a plastic bag that it sits in, so not wanting to stain the contents of the personal survival kit i'm thinking I may dip the entire nitro bottle in was to seal it or better yet paint it with fingernail polish.