.u goes in:

/UTGame/Published/CookedPC/Scripts/

.ini goes in:

/UTGame/Config/

Mutators are added through the command line with each mutator being separated by a comma and NO SPACES.

?mutator=TitanTeamFixUT3.TTeamFixMut,ServerAdverts.UTMutator_ServerAdverts 

You can also add mutators in the web admin or vote them in in (if you have the 2.0 patch) but every time the server is restarted you need to re-add them.

This is what our command line looks like for our sniper server:

[size=7:8eff23af7e]server DM-Deck?Game=UTGame.UTDeathMatch?GameMode=0?ForceRespawn=1?NumPlay=3?TimeLimit=20?GoalScore=30?mutator=dFb_MutPack1bnf.dFb_Spawn_Protection2nf,dFb_MutPack1bnf.dFb_StealthTrans2anf,dFb_MutPack1bnf.dFb_Ultra_Rifle7cnf?GameSpeed=1.2?AccessControl=dFb_AccessControl.dFb_AccessControl -login=XXX -password=XXX -multihome=69.65.59.226 -port=7777 -log=69.65.59.226-7777.log -queryport=6500 -nohomedir -unattended[/size:8eff23af7e]