Can someone please tell me what I need to do in order to have secondary interfaces on a Cisco report themselfs as the alias IP rather than the primary interface IP address in a traceroute?

This is a confusing way to state the question...it implies some standard for what it means to "report oneself as an alias IP," and I think you will find that there is no standard interpretation of that language.

Example:

FastEthernet 1/0/1 has a primary address of 10.1.1.1 It has a secondary address of 172.16.1.1

In a traceroute, where it would be expected that the box report itself as 172.16.1.1, it is reporting itself as 10.1.1.1

Is there a way to remedy this situation and have it report itself as the IP address that is actually being used for that flow?

No. Upon receipt of the packet, a router (R1) does not have any data about what IP address the prior hop (R0) may have used to decide to forward the packet to R1. It merely knows that it came in on that interface, and might now a MAC address if it was a multiple-access interface. So R1 can only send ICMP time exceededs (traceroute responses) from one address per interface, and it chooses (rightly so) the canonical, primary address of the interface. If you wanted to acheive this functionality, you could do it with tunnels, wherein the rotuer would receive the traffic on a tunnel interface with your 172.16.1.1 address. --jhawk p.s.: Is it asking too much to request people identify themselves by name?