Hi Kiran,
I would recommend to connect your branch office to the Router of the Head Office than the Layer 2/3 switch ( i assume that the L2/3 switch is part of the distribution/aggregation layer of your topology).
So, when this branch office needs to communicate with an other branch office via the Head Office the traffic to be routed only by the router than to pass via the L3 switch to the HO router and then to a remote differnet Branch site.
Furthermore, it could be more easily to apply a common security policy if all the Branchs are connected to to the HO (Head Office) router. Finally, in respective of routing it will be easier to handle all the routes to your HO router only.
Hope that helps,
Vasilis