If samashrayanam is performed through one Acarya and bharanyasam through another Acarya of the same mutt, then whom should we consider as our Acarya? Please clarify.

Even if samashrayanam and bharanyasam are performed by different Acarya-s both are considered as Acarya-s. There is no restriction that one must have only one Acarya. Bhagavad Ramanuja had five Acarya-s.

So, one should worship all the Acarya-s, and recite their thanian-s.