I see you're troubled by the same thing as everyone else, so I'll use this chance to talk a little bit about how Japanese writing system looks like and why it looks the way it looks :)
First of all, let's examine the sets of symbols in Japanese.
ひらがな(hiragana) - a set of 46 wiggly symbols which expand to 106 sounds. It's an awesome example of data compression - 106 syllables pummeled in only 46 symbols!
カタカナ(katakana) - a mirror copy of hiragana, if you can pronounce one, you can pronounce the other. There is a twist though, katakana has some expanded combinations due to it's use in foreign words, but these rarely appear and you won't have to care for them until you're good enough to ask a Japanese person to explain them anyway.
漢字(kanji - Chinese ideograms) - Now these are fun. One might think that minimal Japanese kanji set contains over 2000 characters, but that's just a matter of perspective and old-fashioned way of thinking(will write about kanji in more detail later). Indeed, there are at least 2000 kanji in daily use, but! The actual number of symbols involved is smaller by an order of magnitude.
Arabic numerals. Yes, they use arabic numerals just like anyone else in the world today. Of course, one can write numbers in kanji, but that's like writing fifty one instead of 51.
Let's see how these scripts fit together. Because kanji are the core(they contain ideas), we'll start from kanji. Consider words death, to die, died(pardon my morbid association). They all have something to do with death. In Japanese, such inherent ideas are contained within kanji. But, kanji themselves carry no grammatical meaning. Writing 死(death ideogram) alone won't suffice if you want to expand on the idea.
That's where hiragana comes in. Hiragana forms all the grammar-related structure(and some content too!) in Japanese. In an example, death becomes 死(no hiragana attached), to die becomes 死ぬ, died becomes 死んだ etc. It is what makes the distinction between different grammar forms with the same basic idea. There are also some content words written entirely in hiragana but you'll know them right away when you see them.
Another pain in the ass(and this really is a pain in the ass until you get used to it) is the fact that kanji make compounds. On one hand, this is brilliant compression(imagine having a different kanji for every compound!), but on the other, it creates a lot of confusion when you try to read them(more on that later). Some examples would be 死者(death + person=dead man) 中心(inside + heart=centre) 国境(country + border=national border).
Katakana, luckily, is as straightforward as it gets. Used to write content words of foreign origin, swear words or coined slang words.
Now let's try and read something. as you may have already noticed, there are no spaces in Japanese so one's biggest hurdle when starting to read is figuring out where one word starts and the other begins. For the sake of orientation, I'll write a few generalized 'rules' and their possible exceptions.
1. Beginning of every katakana blob is the beginning of a new word. I can't think of any exceptions to this one which means I never encoundered one or there really aren't any.
2. Beginning of every kanji blob is the beginning of new word. This holds for but a few examples such as the honorific お(o) or ご(go) which can be written in hiragana.
3. Hiragana を(wo) can never be a part of a word, amen.
4. Little hiragana つ(tsu), っ is always in the middle of a content word written in hiragana unless used to represent a colloquial pronounciation such as cutting off the grammar suffix.
5. You'll never be able to read Japanese by following these rules so don't learn them by heart; it's a waste of memory. Use them in situations where you are not really sure what's going on.
The second problem we encounter when reading is kanji pronounciation. Unlike hiragana and katakana, a kanji does not necessarily have a set pronounciation(in fact, very few of them do!). Instead, every kanji has multiple pronounciations divided in two kategories, kun-yomi and on-yomi.
Kun-yomi is the Japanese reading of a kanji and is used most of the time with stand-alone kanji or words containing only one kanji and hiragana suffixes/prefixes.
On-yomi is Chinese reading, the way Japanese heard and approximated it. It really has little to do with the way Chinese characters are read today(there is a resemblance though). Such readings are used in majority of kanji compounds. There are exceptions which you'll just have to catch along the way though.
If you have any further questions(and you should have them!), don't hesitate to ask :)
Also, if you haven't started learning hiragana yet, you should get to it as soon as possible. In other words, now.