If you use the items often or in critical situations, store at point of use, even if the items are unmatched. Otherwise, store like with like. Doubles are handy but a little extravagent depending on one's budget. Label on all sides and on top. Also label were the item goes back to if you are forgetful like I am.
When buying containers, make sure that what you are storing will in fact fit into them and likewise that shelving, if the shelves are "fixed" , will accomodate the containers. I found "tote boxes" large enough but only two could fit on a certain shelf system because of the location of the support columns but with another brand, three could fit. These shelves were the same size. Also, decide if you want handles that protrude or not. Also, sometimes cardboard boxes are really advantagous. Often free, you can find like-sized boxes and stack them and make a hole in the front to put items in as you find or sort them. That way you don't have to pull them out and remove the lids.
Beware of over-subdividing, espeically on things that are not used often.