Well the easiest thing to start with is your tranny fluid level. Since you have the 545RFE (which by the way is one of the most reliable transmissions in Chrysler products), you have a dipstick so you can check the fluid level. Here's the procedure: http://www.wkjeeps.com/wk_maintenance.htm#TRANS
If the fluid looks good (not burnt/brown) and the level is correct, your best bet is to take it to a stealership because you're under warranty. Is your check engine light on and are there any other issues with the tranny when you're driving? I feel that your transmission fluid level is probably low because harsh shifts are usually caused by incorrect line pressure. If you find that your fluid is low, check for leaks around the transmission pan gasket and the cooler lines going to the radiator because these are the most common areas where the 545RFE leaks.