I had the same issue with mine (along with many others on the forum). It sounds like the dealer did not enable the relays for the turn signal/brake lights. You will have running lights without these relays, but no brake or signal lights. Kind of important! Haha
You should be able to find the directions for the 7-way wiring harness online. Try going to leeparts.com
If your dealer is like mine, you will need to bring the directions with you. Most of them think these are plug-in-play.
2006 Commander, 4.7L, QT2, Dark Khaki, - RR 2.25" lift in front, OME HD springs rear, 265/70 Goodyear Wrangler Duratrac (no spacers, original wheels), OME shocks in the rear, Bilstein HD front struts, 4xguard: front guard, belly guard, side guard 2, & rear sliders. Skid plate group with front two hooks, heavy duty tow package, AFE CAI (dry filter)