Quick answer...
By Evil areas you mean:
Neriak
Ogguk
Paineel
Cabilis
Overthere
Main factions you need are the guards in each area obviuosly.
Paineel is easiest, kill in The Warrens all manner of Kobolds. You lose faction with the Kobolds and raise it with both Heretics and some of the Erudin groups.
Cabilis: Check these factions in the Bestiary (sic), there are several posts about raising these. It is a daunting task for non Iksar.
Ogguk: Raising guard faction (by killing stuff) here might destroy good factions. Most non Ogres don't need to go there, and the ones who do (enchanters) have ways to avoid being KoS.
Trolls and Dark Elves are not KoS to the guards at least initially. Keep in mind inside the Ogre/Troll SK feud might make a Troll KoS.
Neriak: See
this thread (scroll down to my primer ahem)
Overthere faction is another one that has several posts. Look at the Sarnak War braid quest in the Overthere Quest section.
Other evil areas are the Qeynos Aqueducts and Freeport Sewers but these can also be avoided if need be.
Do a bit of poking around in the faction section of this site.