This is a quilt that I have been working on.
You can see the heavy white cotton thread that I have been using to tie it all together in the pic if you look close. Its down the left side, and along the bottom. I just went from spot to spot and then cut in between. Still took a while.
BlondGirl is right, this is about the easiest way to do it. If your spots are to close together to have enough to tie with, make sure to leave some slack. I like to put my quilts on a big hoop when I am doing the ties, it makes pushing the needle through much easier. A sailors palm or a thimble can also help.
Longer hanging ends will make it easier to tie (looks at hands cut up by pulling on heavy cotton thread), much easier.