if you know the word look for usage on the net, more commonly the kanji will be used but there are still quite a few words that have kanji but the kanji is rarly used.
You'll learn in time from reading and chatting what uses what kanji.
Kanji are used for the... dunno the technical word for it >.< but like the "core" of words, and the hiragana are used for the grammatical endings - e.g. changing the tense of the word - and for particles... and katakana are used for foreign import words and sometimes to give an added emphasis to a word (kind of like italics).
kanji - most nouns
本、花、学校、自動車
- part of verbs/adjectives that does not conjugate (what Kinsao explained as "core" ) 赤い、健康な、歩く、勉強する
hiragana - part of verbs/adjectives that conjugate
赤い、健康な、歩く、勉強する
- particles
は、て、と、を、が
katakana - foreign (loan) words
アメリカ、コーンスープ、ギター
- onomatopoeia
パタパタ、コトコト、
- scientific name for plants/animals/fish/insects etc.
ツリフネソウ、ツシマヤマネコ、ニジマス、アメリカシロヒトリ
There are many exceptions, but if you start with hiragana and then learn the words with kanji little by little, it won't be so confusing.