It can be done:
Tools > Configuration files > Filetype Configuration > Miscellaneous > filetypes.yaml
Then uncommend and edit:
[indentation]
width=2
# 0 is spaces, 1 is tabs, 2 is tab & spaces
type=0
Save the changes. Default width is usually 4. To be honest, I did this for the Ruby filetype, not for YAML. The company I work for never told me if they want the YAML to be 2 spaces, we have rules only for the Ruby code.
After the changes, you could do:
Tools > Reload Configuration.
Or simply close Geany and open it again, if reloading don't give the desired effect.
Eugene