If the bobbin thread is showing on the top that means that the tension isn't set correctly for the thread being used, So you need to balance it out so that if anything the top thread is showing just a hair on the back,
Generally bobbin thread is used in embroidery, it is thinner and you can fit more onto the bobbin requiring less bobbin changes, the prewound ones are nice as they have just that little more as well. and when doing embroidery you will use up more bobbin thread than you are used to as there is usually a lot of stitched unless you are using line designs like redwork,
Any specific questions feel free to PM me, I have been using an embroidery machine for more than 16 years,