These are two different Agama-s that are followed for Thiruvaradhanam of Perumal.
Vaikanasa Agama was written by Saint Vikanasa. Pancharatram was propagated by Perumal Himfself. Both are appropriate and are followed by the elders.
Vaikanasa consists of many Veda mantras and Pancharatram is full of Tantric mantras.
While Vaikanasa Agama is practiced only by the families who belong to that lineage ,Pancharathram can be initiated to others and can be practiced by anyone accordingly. This is the significant difference while mantras vary for both.