You may be able to close up that very small hole next to the thumb opening by knitting into the back of the stitch. That tightens up the stitch and may help lessen the hole.
For the thumb it sounds like you cast on 3 sts, work those 3 and then work the sts from the stitch holder. Use the stitch holder like the left needle if possible and knit the stitches off onto the right needle. Then go on to cast on the second set of 3 sts.