I just read you posting asking how you avoid having gears run into each other.
the problem is when you start a gear mate... or screw mate SolidWorks creates the mate based on the Models current position. So, you need to allign the to componets correctly before adding the mechanical mate.
to allign the two componets you could either move them mannually or add another mate to get them were they need to be and then supress that mate. The addvantage to using another mate and suppressing it is if you need to make changes you can also unsupress and then supress that mate to jog your parts back to their starting location.
I hope this was a help,
Al Whatmough
SolidWorks Training & Tutorials on DVD - Inspirtech - Home
Video Based SolidWorks Training
Now get Training Bundles that include a 3D SpaceExplorer