How do I “fix my permalink structure”?

I asked a question, well a few questions, here:
http://wordpress.org/support/topic/365290?replies=1#post-1398786
The guys who answered helped me solved the last three bu the first question, I still don’t understand what he means – “permalink structure looks wrong” – how do I correct this? I tried fiddling with some settings under Site Admin -> Blogs and now the whole blog is down (I’ve just posted a question about that). It would be great if someone could give me a step by step solution to this problem. You’ll probably will need this:
http://wordpress.org/support/topic/365290?replies=1#post-1398786
And this is my site:
http://www.thewebsiteofdaniel.net