Subordinate means putting one thing below another––a subordinate is someone who works for someone else, and to subordinate means to place or rank one thing below another. "We subordinate our desire for popcorn to our desire to keep watching the movie."
The ordinate part of subordinate refers to an ordering of things, and sub- means "lower." "In the army, a private is subordinate to an officer, whether that officer is his direct commander or not." When it's a noun or adjective, the word is pronounced "suh-BOR-duh-nit," and when it's a verb, "suh-BOR-duh-nate."