1) For this method of joining, I do not quilt near the edge of the sections. I give myself at least 1" between any quilting and the edge of the quilt. See where the screw driver is pointing to? That is as far as I quilt until after the sections are joined. Believe me, it will just be easier to handle if you join the sections the way I am with this quilt.
2) Trim all sections carefully - the backing, and the quilt top should all be exactly the same size. The batting will be trimmed 1/4" more by hand once the sections are joined.
3) To join the quilted sections together, use lots of pins. You are joining two sections with right sides together and are only sewing the quilt top edges together.
Pin the edges together and then pin the batting back and out of the way so you don't sew it accidentally. Pin more. Don't even attempt to join two large sections without pinning it to death. And then add 2 more pins! I guarantee that you will not be happy with how everything lines up (or not!) if you don't use all the pins you own.
4) Once the sections are attached, I lay the whole thing out on the table and trim any excess batting between the sections with scissors, being very very careful not to cut any fabric. I trim the batting in a slightly wavy line, which I like to think prevents the join from being too visible. I'm not sure if it effectively does that or not, but it's what I do. Then I hand stitch the batting together using a ladder stitch. When all of these steps are done well, the batting will lie flush and flat, with no gaps along the join.
5) The last step is to fold over at least 1/4" on the edge of one panel and hand stitch/applique it on top of the other panel, just as you would stitch a binding edge. I like to do this by hand so that there are no stitches on the front of the quilt from the join.
6) Once the seams are all finished on the back, then you can add more quilting. I plan to quilt all the horizontal seams from one side of the quilt to the other, which further holds all the batting sections together. And then I'll probably do more quilting... the blocks are heavily quilted, so the sashing will likely need more quilting.
Quilt-as-you-go is a construction method I enjoy since it allows me to do all my own quilting, even on the largest quilts. These are two of my other quilts I have finished using this technique - Swoon, and Scrappy Memories.