This is done with the help of the Shirabe brush, which allows you to draw a route for your human partner to travel along, while Chibi himself takes a different path. One example that was cited in Famitsu magazine a few weeks ago was that of an old bridge. The game required — presumably because the bridge couldn’t support the weight of both — that Chibi cross it by himself while Kuninushi found a different way around.
It’s an interesting and obvious design choice but it does raise a few questions. Working on the DS should certainly mean you have more direct control of the brush. However, every Celestial Brush in the original Okami allowed you to control different elements such as wind or fire, with which you could indirectly influence the things around you. The Shirabe brush, however, gives you direct control over a character. I wonder if it will be passed off as a design choice you don’t question or if Capcom will provide a reason behind its power.