If you want your time entries to use bill rates defined for the activity item rather than the employee, you can set that in the Projects screen using the rule Use bill rates from Activity Items screen. Check the Core Help for more on assigning rules to projects. Furthermore, you can set Core to automatically apply this rule to all new projects by selecting the option Use rates from activity list in Global Settings > Master Information. Check the Core Help for more on that. To know more about the rate hierarchy in Core, check out this article: Rates in Core.