If it is pointed out that in all (srI shankara) matams, only the Chandra MoulIswara pUjA is conducted, [*then the answer is that*] it is because of a specific reason.
ParamEshwara Himself gave five spatika lingAs to AchAryAl and wanted Him to ensure the ArAdhanA for them, for ever, in this lOkA. AchAryAl had ensured that uninterrupted ArAdhanA by keeping the two out of five in the matams at SringEri and kAnchi and the remaining three at the temples of NEpAl, kEdArnAth and Chidambaram. When we say 'Sankara Matams', should there not be 'uniformity' amongst all of them? That is why He introduced Chandra MoulIswara pUja in [*all His*] matams.
Lakshmi Narasimha Murhty gave a 'sAlagrAmam' to AchAryAl. As IshvarA Himself had given a spatika lingA, which is [*considered to be*] His SwarUpA, Narasimha Murhty also gave a sAlagrAmam, which is of His SwarUpA. As He has kept the spatika lingA in the pUjA of the matam, He has kept that sAlagrAmam too in the pUja.
He doesn't entertain the Siva-Vishnu Bhedham, even a bit. As He has done the spatika linga prathishtA at Chidambaram, He has done the NArAyana prathishtA at BadhrinAth. There itself, He had establihed a math. Among the places where He had established the matams, Puri JagannAth and DwarakA are important Krishna kshEtrAs. He has not commented on Siva sahasranAmam; instead He wrote a bhAshyam only for Vishnu sahasranAmam. Though there are many gItas in our purAnAs such as Siva gIta, dEvi gIta etc, He has chosen to give a bhAshyam only to the gIta, presented by Krishna ParamAthmA. As He has composed devotional hymns towards IshvarA and ambAl, He composed on MahA Vishnu, srI RAmA, Krishna and Maha Lakshmi also.
As all these points are not properly considered, He is interpreted to be a saivaite [*albeit wrongly*].
What is being conducted [*daily*] in AchAryAl's matams is not only [*an exclusive*] Siva pUja. As I mentioned in the begining, the very panchAyathana pUja is the pUjA of the matam too. AchAryAl is the combined avthAram of IshvarA and ambAl; Uma and MahEshwara themselves gave Him the pancha lingAs at KailAsh; that is why He established Ishwara and ambAl as the main deities of the pUja of the matam. But still, as per Siva panchAyathanA, even Maha Vishnu, Ganapathy and SuryA are also present in the pUja. Here [*in the matam*], similar to Siva rAthri and nava rAthri, we celebrate rAma navami, gOkulAshtami, Narasimha jayanthi etc also [*in the same scale*].
Whenever srImukams  are issued, from the matam, what do we [*the presiding AchAryAs*] say? In that, we say, for a particular activity, "kriyathE nArAyana smrthihi". That is, any book or an activity [*sacred or secular*], for which this srImukam is issued as a token of blessing, to become a success, we say that 'we remember NArAyanA'. We don't say that 'we remember Siva'.
What do I say when you prostrate before me? I say only, "NArAyana NArAyana". All the shankarAchAryAs also say only so. This is the rule made by the Adi AchAryAl Himself. Inorder to get the good [*and auspicious*] things to happen to this lOka, He has ordained the remembrance of NArayanA only, as He is the sustainer of this world (jagadh-paripAlana-karthA).
For so long, I was talking about the existence of the impression that advaitins are saivaites. Diagonally opposite to this, there are some who hold that Sankara worshipped only MahA vishnu. They quote this NArayana smaranam and Vishnu sahasranAma bhAshyam etc as the supportive evidence for their claim. In addition to that, they also point to the fact of establishing the Ishvara or the saguna Bhraman, which does all these lOka-vyavahAra, to be none other than NArAyanA Himself, by AchAryAl, while elaborating about Him [*Ishvara*] in His BhAshyAs.
 The message/foreword/blessings from the presiding AchAryA of a Shankara Math, in the official letter head with the seal of the math is known as srImukam.