Keep in mind I press my seams to one side so if you press your seams open you probably don't have this problem. To start you will want to sew your seam just like normal. Then lay your piece on your pressing surface. The side you are pressing your seam to will be facing up.
Then you are going to press the seam. Be sure to press DO NOT use the back and forth motion you use for ironing clothes as this can stretch and warp your fabrics. I use a dry warm iron when I press my seams. When I first started quilting I used steam like it was my best friend. I later found that this too can cause your fabrics to warp and become distorted. I know some people still prefer steam-I do when ironing my fabrics prior to cutting just be careful if you chose to use steam.
Now open your fabrics and press in the direction you want your seam to go. This should leave you with a super flat, super crisp seam.
Please don't judge my ugly ironing board cover. I really do have every intention of making a new one someday. It's just one of those projects I haven't found time to get to yet. And I'm sorry the photos are a little blurry I took them on my iphone a while back to help out a friend.