Most supermarkets have such plastic containers, in an assortment of sizes, on sale in their kitchen department. They are cheap yet ideal for the job. Be sure that they are of the softer plastic type and the lid seals securely. The stiffer plastic type will be sure to break in time and upset your day. Once you have your many containers, use a permanent marker pen to clearly label the lids and sides as to what is inside.
Rice is an excellent moisture absorbent and helps keep the contents dry and rust free.
Containers can then be placed in a canvas bag, or stacked in the Nally box. I find over time I have collected so much gear it is ridiculous for me to take it all on each trip. To this end I have made up one all-round kit of bits and pieces I take with me on every trip. I then load only the gear I require for the particular style of fishing I intend doing. This cuts down the amount of fishing gear in the boat, yet if something different comes up, I can usually make a rig up from the bits and pieces to get me by.