It's been said over and over that you don't want to leave the solder paste opening wide open for a QFN center pad. 50 - 75% paste coverage will get you bets results. With full coverage, your QFN can end up floating too high and not connecting with all of the pads due to their significantly smaller aperture.
But how do you create a custom paste layer? In Eagle, it's not terribly obvious, but it is easy. Open the part that you want to customize in the Eagle Library editor. Open up the package for that component. Now, select "i" on the left side and click on the center pad. You might need to turn off the "tcream" layer in order to select the pad.
In the Properties dialog box, un check the check box for cream. That will get rid of the standard stencil layer. Now you can use the rectangle tool to add in stencil cut-outs as you want the. Make sure you set the layer for the rectangle to be "tcream" and remember that you are drawing the cut-outs of the stencil, not the blocked part.
Obviously it will be different for every CAD package, but the concept is the same. As is the need to do so.
The Internet is weird.
There's actually a website for paste eaters.