If they are still warm from the oven, you can gently press down on the tops with a clean dish towel. Or use a cutting board to press down gently.
If they aren't still warm, when you put the layers together just put the top layer upside down (so the flat part is on the top). You might need a little more frosting than usual to fix the edges of the middle part, but once it is frosted, nobody will ever know the difference 
For years I would level the dome. Recently, I picked up the pressing the dome down gently with paper towel just after taking the cake out of the oven. It works well and the cake is the same because you are actually pressing out air that is trapped inside the cake. Next time you baek consider lowering your oven temp to 325 instead of 350 so it bakes slower. That way the outside of the cake which is the hottest doesn't bake faster than the inside.
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