[Old English under-.]
Some terms refer to something being placed—literally or figuratively—underneath something else: underclothes, undercover, undergrowth, underpass. The sense of lower position can figuratively refer to someone in a subordinate role: undersecretary, understudy, undersheriff. Some have lost a direct link to position: understand, undertake.
A related and common sense is of something that is insufficient or incomplete: to underachieve is to do less well than expected; a firm that is undercapitalized has insufficient funds to achieve its desired results; a person who is undernourished lacks enough food for good health; an area that is underpopulated has an insufficient or very small population.