You don't cut the ties at all until after you've put the thread in the quilt unless you're fond of threading the needle. Thread with a very long piece, put the stitch in the quilt, pull it through it's until about three inches from the end, then cut the long thread to match. Go on to the next one. Go back, tie the ends - you can use a surgeon's knot - then trim to desired length.
I'm sorry you are having so much trouble. There are days that make the quilts in Penney's catalog look good, but those aren't made with the love that's gone into this one. Can we see a picture?