You CANNOT USE THE CAR SEAT OVER THE WEIGHT LIMITS! They are there for a reason, that is the max weight the car seat passed crash testing with the harness. If you use it over the weight limit, you are playing with danger, as the harness was only tested and passed at 40lbs, anything over that the integrity of the seat will be tested.
If her shoulders are over the top harness slot, you MUST STOP USING THE HARNESS! If she is over the weight limit you MUST STOP USING THE HARNESS! These aren't suggestions, these are set in stone, and are there for a reason. It is extremely dangerous for her to be using the harness over the weight limit ,and she's at a very serious risk for spinal compression if her shoulders are over the top harness slot, even in a minor collision.
Also, you CANNOT USE WINTER COATS OR BULKY CLOTHING in the car seat! In a crash, these things will compress, leaving the harness loose and subjecting your child to ejection from teh car/car seat or being thrown violently forward too far.
The combination seats like the Eddie Bauer make terrible booster seats. The seat is too wide and the belt path puts the lap portion of the belt over the abdomen. SEe the picture in this article, this is an Eddie Bauer combination seat. See how poorly the belt is fitting this 5yr old, the shoulder portion is way too low and the lap portion is up on her abdomen. http://blogs.consumerreports.org/cars/2009/12/iihs-rates-... In a crash, this girl would have her torso thrown forward and her abdomen would stop the belt.... nothing but soft tissue until it hits the spine. This is called SEATBELT SYNDROME, please look it up.
Purchase a dedicated booster seat for her. You can find a very good high back booster (always go high back for her age group) for $50 at Wal Mart. The Graco Turbobooster fits kids very well and will last her until she is old enough and large enough (8yrs old, 4'9") to sit in the adult belt alone.
I'm honestly shocked that anyone would recommend you continue to use it. 9 out of 10 car seats and booster seats are installed and used improperly, which is why car accidents are the #1 killer of children in the US. Please read the manual, install the seat properly, and use it properly every time. THe Manual has all the information you'd ever need to use the seat properly all the time.