You can go into your settings and change who you auto target. I changed it so that the only enemies I focus on are the ones aggroing on me. When I press X it goes to a party member first (unless I get attacked, which rarely happens first off if you're healing correctly); I cycle through them with up or down, and can highlight an enemy with < or >. You can also set it to include party members, pets, and NCPs.
When I did CT for the first time, the other Alliance bars literally configured right across the center of the screen. I still have no idea what happened in that first CT because I didn't have time to fix it.
