In a previous post I showed how to build a complicated molecule with Avogadro. Here I show how to build it in 2D first and then convert it to 3D.
I use PubChem Editor to build a 2D structure and insert it into Avogadro using the insert SMILES option. JChemPaint is another free option for drawing the 2D structure.
Avogadro does not process the chirality info (the @ signs) in the SMILES string correctly, so some more editing is needed. Hopefully this is fixed in future versions of Avogadro (I use 0.9.5).
There is some discussion over at Rich Apodaca's blog about whether building in 2D or 3D is easier. Try for yourself and make up your own mind.
Update: the program Marvin Sketch can also be used for 2D to 3D conversion, and the chirality info is interpreted correctly.