How do you change atomic valence in Avogadro?
While there are some automatic valence features in Avogadro, you can always turn them off. Bonding is mostly a matter of appearance.

For example, let's import $\ce{IF7}$.



Notice that the central iodine doesn't show enough bonds. So we'll draw some in. Switch to the draw tool and turn "Adjust Hydrogens" off.



Now just draw connections between the atoms. Voila!