My zippers always used to look less than stellar. They would get bunched up and stuff at the ends where the side seam was. I recently found out a secret though, I'll try to explain it with pictures.
This assumes you know how to make a simple zipper pouch the traditional way that I was taught.
1. Sew a little square of fabric on each end of the zipper. Cut 2 squares 2" x 2" and fold two sides into the middle, then fold it in half again so it's 1/2" x 2". Then sew then end of the zipper in it and trim the extra off of the sides. Do it again for the other side.
2. When you cut your lining and outer fabric make sure they are an inch longer than your zipper with the fabric ends. This means you are including a half inch seam allowance on your fabric but not on your zipper. When you sew around the outside(red dashed line), with the two lining fabrics together and the two exterior fabrics together, you do not sew the fabrics ends on the zipper into the seam. (I didn't show where you would leave a gap in the stitching so you'd be able to turn the whole thing right side out)
3. This is what the ends will look like close up when you turn everything right side out. The gap that shows in the picture is unrealistic(it's a tight fold, nothing is going to fall out through it) but I was just trying to illustrate the idea better.
If I explained something in a questionable manner let me know. Also if you're completely confused then you might not make your zipper pouches the way I assumed you do, in which case disregard this or I can try to draw pictures for the whole process