i let the thread i'm going to tie with double as basting.
depending on the size, i'll either drape the unbasted sandwich over an ironing board or the frame in front of me. sometimes i spray baste first, sometimes i don't. depends on the mood i'm in that day.
[because i'm right-handed] i start at the right edge. i poke the needle up through the sandwich at the spot for the first tie, then back down about 1/8th inch to the left. i proceed in a line to the left, spacing the top "stitches" close enough together to secure the layers. the "giant stitches" underneat are kept fairly loose.
because the thread (usually #10 crochet cotton) is thick, the top stitches hold it all together nicely even when the bottom stitches are long and loose.
when i'm done, i turn it over, cut the "giant stitches" in the middle and c'est voila! there are all the little threads ready to be tied in knots. if i do bows instead of plain knots, they get a dab of washable fabric glue in the centers to make sure they stay tied throughout use and laundering.
it's important to keep enough slack in the bottom to leave at least 2" long threads after they're cut. any shorter and you might need to tie with tweezers. OY!
if i'm knotting a quilt made from 2" squares, i knot as i go, but still don't cut anything until i'm done.