When using a Standard Mode Agent Pega handles all resource locking and transaction management for you. Also Standard Mode Agents do not require nor do they use the Authentication Service configuration in the Security Tab of the Agent Queue Rule. As a result Standard Agents are easier to manage and configure. As a Best Practice we recommend always using Standard Mode Agents.
There are exceptional circumstances when a Standard Mode Agent does not provide the level of control over resource locking and transaction management that you may need (i.e.: distributed transaction management, advanced POJO or EJB integration, invocation of DB Stored Procedures). In those special cases you can use an Advanced Mode Agent instead. When using an Advanced Mode Agent you must manage all resources locking and transaction management yourself. Also Advanced Mode Agents require and use the Authentication Service referenced in the Security Tab of the Agent Queue Rule. For example, if you are executing Custom Java (also a violation of best practices) or RDB- Methods (a better practice is to always use OBJ- Methods) in the Activity referenced by the Agent then you may need to use Advanced Mode for the Agent to function properly.