What are agents in the matrix and what is their relationship to sentinels?
Agents in the Matrix are sentient 'programs' designed to remove threats from the system. They can be thought of as an Anti-Virus solution within the Matrix program. 

Sentinels are physical squid-like robots in the real world outside the matrix whose aim is to destroy and capture remaining human settlements.

There is no direct relationship between Agents and sentinels except that they both work for the same entity against the humans.