I assume form your post that you are using Makerware? Here are a few pointers:

- you need to set the 'object' to left extruder.
- You need to select the correct printer profile i.e. dual or single.

The printer will not switch to a different nozzle due to a clog so don't even go that route. Its 99% perent chance that its one of the above. You also don't say if you have used the left extruder before.