Scroll down to the bottom. start at any file labelled 01 then either movie on to a file of a different type that's also 01 and only movie onto 02 once you've looked through all the 01s. OR you could follow one "file type" from 01 to their end and then cycle back through each file type like this.
What I did was cycle through all the Lain related files in order, then did all the touko ones, and then did all the disks like "Tak & Ekm" files. I'm sure some people would cringe at this but I think I got the full effect of the story even if it didn't turn out "linear".
I'd say just go with what interests you first and then go through the ones you're not as enticed by later. It's a slow moving story so once you get farther in it and start asking questions it'll shed new light on some of the older files you may of not been as interested in. Once you go through all the desired files on Site A then click on "Change site" and you'll get to the second half of the game.
It's not a conventional method o storytelling or even convenient but nothing about Lain is. I have to say that I really like the idea of sifting through someone's files and slowly putting together a story though so I heavily enjoyed the content and the format.
Hope this helps!