if your bottom thread is showing on the top you need to either tighten the top tension or loosen the bottom tension...the key is finding that magic setting where the top and bottom are equal. if you match your bottom and top threads those spots do not show up so much, but finding the correct tension would be the best way to go.
it is always easier to adjust the top tension so start with that, turn it just a little at a time and stitch a few inches, check, adjust, until your stitches are the same on the top and bottom.