The first thing you could try would be to lower your top thread tension down just a little and see if that stops the bobbin thread from being pulled up to the top of your embroidery. Lower abit and then test stich a design
You may have to make this adjustment a couple of times to get it to where the bobbin thread is not showing on top.
But make sure your design is still stitching out nicely.
It sounds as if your top thread tension is set too high and it is pulling the bobbin thread up.
There should be a place in the settings of your machine to lower the top thread tension or increase it if need be.
When embroidering on cotton you could also starch the cotton before embroidering.
Spray with spray starch and then iron and then spray again and iron. This will give more body to your cotton. This would not have any affect on the bobbin thread showing!
Denise in Calgary