If you're making an infinite runner, you're really going to have procedurally generate your levels -- because they're actually infinite, and it will save you tons of work designing levels. The key is to generate your obstacles in such a way that they don't overlap, which is entirely doable, I'm sure. Provide some more information on your setup, and someone on the forums should be able to help you with that.
EDIT: As an aside, layout size doesn't appear to be limited to 10000 pixels, so I'm not sure where you're hitting a wall.