Hi,
I can confirm that this is not possible to apply a feature template to a feature that already exists using the current version of ArcGIS Explorer Online.
timor - we are planning on making improvements to feature selection and symbolization in a future release (no timescale at present though) which may help you.
codybrown - please can you elaborate on your workflow so i can get a clearer picture of what you are trying to do? Are you talking about features coming from a ArcGIS Server feature service?
Mike Rudden
Esri