Weave in ends going across the work (parallel with a row).
Seam them using a needle threaded with yarn. If you gently open the stitches by pulling the fabric widthwise, you can see horizontal bars in between two stitches. With your needle, go behind each bar, alternating between sides so you sort of lace up the side, then pull the yarn snug. Not tightly, because you don't want to pucker the bootie, but pull snuggly none the less.
Hope this helps!