MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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They cross. It's no big deal. They don't mind rubbing. However, it does seem to rub the fur the wrong way on some folks. (Particularly people who have never built or used one.) It's just not worth worrying about. As to the best place for them to cross I have no opinion.

And no, I do not find belt dust on the table below where they cross on my bots. The belts see far more wear running over the pulleys and from any contact with pulley flanges then they see passing by each other. It most definitely will not be a source of belt wear and most definitely will not cause print artifacts. The belts are not under extreme tension.