Full credit to http://www.flickr.com/photos/blipfish/
Ah... I've been at this point - it's just a process of learning a new camera, so have no fear - you'll be photographing the socks on a flea before long. ;)
I suggest opening the LCD viewer rather than the smaller viewfinder as there's information onscreen you'll want to look at while doing this.
1. Dial in to "M" (Manual mode)
2. Press the 'flower' button on the front, side ring of the lens housing.
3. Press and HOLD this button a second time... gets you from Macro mode into Super Macro mode - your display will show it go from an icon of a flower at the top to a flower with an "S" in it. You're now in Super Macro Mode.
It's at this point the fact that you're in Manual mode will probably show up... your scene might look way dark or too bright. So, use the 4-way thumb button (the one with the up/down/left/right arrows on the right side) to adjust the speed and exposure settings until you can finally see something in the viewfinder decent.
Now, let's say you're photographing an ink pen or pencil on your desk...
There's no doubt your camera needs to be right down there with it... your lens (now that it's fully extended since you turned the power on) can even touch the pencil... it can be THAT close.
Just turn the camera a little sideways now to begin looking down the length of the pencil. Notice how about an inch or so away from the lens starts to come into focus?
For a basic start - just press and hold the shutter button until you see the green box and beep - this tells you you've gotten a good focus.
If you were taking advantage of pushing the MANUAL FOCUS button and using the 4-way dial to focus (using that fuzzy square)... don't be surprised if all you have to do is dial it up to 1. This is super-macro, after all... it's close. You'll be able to tell this because a 'meter' scale appears on the rigth side of the display. It rises and falls as you adjust with the 4-way button.
Note: The way I found out that the S2IS has such a good SM mode is I had dust on the front lens and it was interfering with my focusing. I was actually focused on the dust on the glass itself! So, make sure your lens is clean.
This is basically what I did for the dollar bill shot that I took (linked above).
Manually Focusing would have given me more options as to WHERE the focal point would have landed on that bill (further away from the green emblem, closer than the emblem, etc.). So, you have a little latitude if you wish to use the Manual Focus feature as well.
Let me know if this gets you closer or not? It's a fun (and very nice) feature and there's no reason you won't be using it right away. :)