If I run vpls over l2tp over ipsec will vpls be encrypted?
Yes, but why would you want to do that? There are no benefits running VPLS over L2TP over Ipsec. You could just run EoIP or Gre over ipsec.
I am running vpls over l2tp because i am bridging voip devices over the internet.
l2tp is then encrypted using ipsec transport mode.
the ip phones will get voice vlan dhcp from the main branch and all tags and priorities will remain intact over the tunnel. 
As I mentioned EoIP would be more suitable for bridging networks than VPLS over L2TP.
Dear mrz,
can you please tell me technically why it is more suitable?