When do you use what word to express that something consists of something else?

Here are some thoughts:

• "composed of" refers to the parts of a thing from the point of view of the subject
• "comprising" or "comprises" (not "comprised of" though ardent descriptivists will gnash their teeth at me) can refer to either.
• "contained in" refers to the container from the point of view of its constituent parts
• "consist of" or "consists of" refers to the elements of a thing, with the added implication that these elements are sine qua non — without them, the thing would not be what it is.

There are some works relating the relatively mature field of mereology to natural languages; Wikipedia barely mentions them. I am not an expert on this particular crossroads, but I'm afraid that the ambiguity of natural language won't let you find hard and fast rules as you request. "Parts: A Study in Ontology" by Simons 1987 is the work that I know best about this, and you may find it useful if you are interested in a detailed study of the matter.