Thicker battings are always harder to machine quilt.
If you do change the batting, I would recommend heavily starching the backing fabric (and spray starching the top) before layering again; it helps a lot to prevent tucks and puckers. If you stay with this batting, spray starching both top and bottom may help.
You could try ironing the quilt sandwich to flatten the batting (unless it is all polyester, in which case it could melt!). Someone posted about doing this to reduce bulk under the arm of the machine.
What batting specifically is it that you are using? I assume you are FMQing?