You will need to debug the skin in IE6. That's not a fun task. You can use techniques similar to those found in this tutorial:
Troubleshooting
DotNetNuke Skins to find the problems.
If you look at the Minimal Extropy skin, you will see examples there of how to include specific skin files to make small corrections for specific browsers. You will need to add a css file for IE6 that include just the changes to make the skin work for that browser.