Well for a start it seems you are confused about the meaning of 'word'.
A kanji is not (necessarily) a
word. The ON reading of a kanji is not (necessarily) a
word. (kun readings usually are but that still doesn't mean "kanji reading" = "word".
)
As for knowing which words are common, WWJDIC has (P) tags on 'priority' words but really (as said earlier in this thread) the best way to know a word is 'common' is because you often come across it when reading.