doe,
There are different ways to finish a quilt. The way you choose to finish it might determine how to stack your material. If you want to use binding around the edges to finish it, then you would want to layer your material with the finished or right side of the material facing out & have the batting (if you are using batting) sandwiched in the middle next to the wrong side of fabric. The layers can be basted together by hand with big stitches or use safety pins every 4" or so to keep the material from shifting or bunching (it helps to have a large flat surface to work on). You would then finish it by quilting or tying & then using binding around the edges.
On smaller quilts or baby blankets you might try turning the quilt. This method might work better if you're tying instead of quilting it. You would do that by taking the quilt top & quilt bottom & putting the right sides together. Make sure they are the same size. Cut the batting the same size & put it on the wrong side of either front or back of quilt (I don't think it matters). Pin them all together & start sewing a seam around the outside edges of blanket but finish your seam so that you leave about a 6" opening or larger if bulky (this is so you can turn it right side out). Trim corners & turn the quilt right side out (pulling it thru the opening so that both the right sides of quilt are showing & the batting will be on the inside. Hand sew the 6" opening closed with a blind stitch. Tie the quilt or loosely quilt it. You can topstitch 1/4" or so around the edges & it makes a nice little border & keeps the edges from rolling. Hope this helps!