Run them down so the gasket is flat the first time, snug them down the second time, then take them to the torque spec the third time.
The main goal is to avoid pinching the gasket and applying un-even torque to the cover before it's fully seated and flat. If you deform the gasket, it's more likely to leak.
If it's sitting square on the locating pins and you snug it down as WJB suggests before torquing, you will generally be just fine.