Depending on your level, there are a few different ways to approach the site. And you've already gotten some good advice.
The original intention of the site is for each level to be a single course. However, there are some short courses which don't fit into categories so easily (Survival Phrases, Introductions, etc.).
Naomi-sensei created a new Newbie Series (which is in its second season right now.) That series is called Nihongo Dojo. It's highly structured and progresses in a linear fashion. I generally recommend people begin with Nihongo Dojo when they get started with Japanese. If it's too easy, then I suggest the original Beginner Series. This was also linear and goes for about 170 lessons. The later lessons are quite difficult (I'd hardly consider them Beginner, actually).
There are some other beginner courses... We just finished up Beginner Season 2 and are now publishing Beginner Season 3. While the grammar doesn't get too crazy, these seasons are designed for practice and reinforcement. We also introduce a lot more vocabulary, colloquialisms and some slang and dialect forms. These levels are non-linear.
One interesting thing we've found is that a lot of people use the site not as it was intended, which has prompted us to change directions from time to time (we'll always be changing and trying new things). A lot of people simply listen to all the current lessons while studying a particular level. I've noticed advanced listeners posting comments on current Newbie lessons and newbies commenting on Lower Intermediate lessons. I think these people are listening for entertainment value as well as their educational pursuits.
I think I'm digressing, so I'll just say again that I usually recommend starting from The Nihongo Dojo and gage your level in relation to that. If it's too easy, try the original Beginner Series. If it's too difficult or you need something to supplement it, the Introductions and Survival Phrases are a great way to ease into things slowly. I'd definitely recommend checking out the new lessons closest to your level and interact with the current listeners. People are very friendly around here and make a lot of helpful suggestions. And again, the Forum is another good place to see what other people are doing.
Here's a link where I touched on some of these things in a previous thread. There might be something helpful in there.
http://www.japanesepod101.com/forum/vie ... php?t=2704
Hope this was helpful!
