Personally I wouldn't recommend running the car while cleaning the throttle body. I think you run too much of a risk of something getting sucked into your engine that just shouldn't be there. I realize you may get the cleaner to flow a little better since the engine is actually pulling in air and all but the risk to me is just too large for the small rewards you may gain.
If you don't have the time or tools to do a full intake cleaning I would recommend just taking off the MAF and inlet tube and just shoot the cleaner right into the throttle body and intake manifolds. Realize though that it would be much better to take the manifolds off and clean them while they are off the car to get them really clean.
Just my $.02
