Acharya Paduka-s should not be kept along with Salagrama deities; the sanctum of Perumal should be separate; the vessels for Perumal should not be mixed with along with the paduka-s of Acarya, so there should be a separate place for both.
To know further on this, please refer to question Q47PUR230002 of Purattasi issue of Sudarsanam for answers.