How to add setParameter in mongod config?
Here's a working example that I just tested using 2.6.6 - I specified two parameters just to show how it is done for reference:

storage:
    dbPath: "/data/db/test"
systemLog:
    destination: file
    path: "/data/db/test/mongodb.log"
processManagement:
    fork: true
setParameter:
    enableLocalhostAuthBypass: 1
    enableTestCommands: 1