You can run more than one but they have to use different ports. So you'll have to configure your firewall to allow each port access to the internet. They'll also be sharing the same bandwidth. So speeds will be divided between the three of them.
You'll only have to download it once but you'll have to install it 3 times on your computer. I have it installed twice on my pc, but I use the same port cause I don't run them at the same time. I have it installed on 2 different accounts.
What i did was downloaded it to C:\Programs, and then installed it onto the different accounts from there. All my accounts have admin priviledges so I could access the program from both accounts.
As far as folders go. Each account will have it's own folders and you can add as many different folders as you like. I don't think you can add folder tabs to the default ones already on LW. i hear itunes is good for organizing files with.
iTunes Tutorial
This thread has info on moving the location of your download folder:
move folder with incomplete downloads
Not sure how it works if you want them all on the same account.
Hope this helps
