With thanks to Michael Lai, who has graciously agreed to help out.  

For those of you who may be finding the instructions on how to set up
your directories on a CS machine a bit cryptic, I've written a short 
how-to which will hopefully get you on your way.  However, I still 
recommend attending at least the first Unix minicourse offered by the 
Maclab in the Reg.

1) Logging In

  I assume that you've managed to procure a CS account.  Once you've done 
that, you need to log in to a CS machine.  You've got two options: a) go 
to the maclab and use one of the linux machines (left side of the lab as 
you enter, often very empty), or log in remotely.  You can find a list of 
available machines here: 
http://stuff.cs.uchicago.edu/searchresults/distro_ver_prefix/3.0/net_group_list/cs_users_college/ips_status/ssh. 
 Note that you don't need to use the same machine, your files aren't 
actually stored on these machines.

  Mac users can use the terminal to ssh (Secure SHell) in to these 
machines: open up Finder->Applications->Utilites, and you should see 
Terminal.  From there, type in "ssh <username>@<machine name>", enter 
your password, and you're in.

  Windows Users: you can use a number of programs for this, but I prefer 
PuTTY.  It's free download available at 
http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html.  Enter a 
machine name and username/password, and you should be good to go.

2) A -Brief- Guide to Directory Structure

  When you log in, you're automatically in your home directory, 
functionally equivalent to Windows' C:\Documents and Settings\<User>.  
-All- your files should go here.  Feel free to take some time to explore 
the hard disk.  You can use "cd" to change directories, and "ls" to list 
files in the directories.  If you're lost and can't find your way back to 
your home directory, you can use this shortcut: "cd ~/".  Incidentally, 
your home directory is often at "/home/<username>".

3) Making Directories

  In your home directory, create the "html" directory by typing "mkdir 
html" and then "chmod 755 html".  Alternatively, you can do "mkdir -m 755 
html".  The "-m 755" part of the "mkdir" command is a shortcut built in 
to the command to set the permissions of the directory upon creation.  If 
you want to see what other options there are for a number of common 
commands, try typing "man <command>".  The "man pages" (short for manual) 
might be a bit daunting at first, but they're very comprehensive.

4) Uploading Your Work

  You should be able to create all the necessary directories now.  Mac 
users can use the instructions provided, and use SCP to transfer files to 
a cs machine.  Windows users can use PSFTP, which is on the same download 
page as PuTTY.

Good luck!