Deodexing allows you to create or use custom themes for the phone. For instance, I know have a custom taskbar which is dark grey, rather than the off-putting white one. This is the link I used for deodexing.
[HOW-TO] Manually deodex your phone. - xda-developers
Some notes that might save you a lot of stress in the long run, if you get all the way to option 4 of the xultimate process and it crashes at core.odex uninstall all instances of java and then reinstall it. Also, for the code part you input after the deodexing itself, I could only get it to work in charge only mode, with the adb drivers installed for that as well.