As mentioned above, you will use it to get access to CWM red when you power up your phone.
This is the procedure you will follow to do so. Look under the section that says "use the following to flash into CWM red"
Here are a few examples of when you might use this:
1) Adrynalyne posted a zip file that fixes incorrect battery readings/fast drains in the EB01 ROM. To apply this fix, you boot into CWM and apply the zip.
2) CWM also allows you to install other zipped ROM's too.
Having to visit every single forum in the forums limits the amount of time I have to keep up on things, but the last I checked ROM Manager is not compatible with the new CWM red, and you do not want to use it to boot into CWM. One of the other guys might correct me on that though.