2010 - 08 - 22
Right click on genomic feature track/P-value track/pairwise comp track, the option with wrench icon allows you to configure plotting style of such tracks:
A panel will appear in floating toolbox with drop down menus and color buttons to play with. Make changes and the track image will be redrawn immediately:
Also, go to "Config & Misc" > "Customize browser display", you will find options to change genomic feature track plotting styles. All options are same as those in toolbox, but this will change appearance of all tracks, and serves as default style.