What needle size are you using? And what longarm do you have? Shredding is usually caused by using a needle whose eye is too small for the thread size, by not having the needle positioned correctly for the machine, or because the tension is not right (usually top tension, but tensioning is a combination of bobbin and top).
It's actually usually good to combine a cotton thread in the bobbin with a polyester thread on top, as the cotton "grips" the polyester and gives you better, more even stitches that poly with poly.
If it's the Glide that is shredding, the issue is probably not the cotton bobbin thread. The top thread has to go through the needle eye many times to form a stitch, so it usually has something to do with that eye and/or the amount of tension on the thread when it goes through the eye.