Application Access with Integrated Security Model

Hi, does anyone have a solution for this situation? Multiple Custom applications that need to have a common profiles for varying permission levels and still be able to maintain an audit trail using integrated security. I know that I can set up aliases and then map the login to an alias to achieve the common profiles . What I do not understand how to do is to discriminate between indviduals using the alias. This is a requirement for the audit trail using the login name. What is the best way to accomplish
this ?
Thanks Bob