Figured this out. Please disregard.
Glad to hear you figured this out. Would you mind posting how you went about accomplishing this? It will greatly help anyone else who has this same question.
I must've overlooked some important information about Network Atlas and ConnectNow originally. I ended up finding the information that would've saved me some time in an obscure note in the knowledge base stating that ConnectNow will only build a topology on Layer 2 information; using a combination of a Bridge MIB and an ARP MIB.
From there I worked with my peers to find another solution that could do topology based on L3 information and arrived at LANSurveyor. We are still experimenting with it but it does have the ability to build a topology based on L3 information, which our new network is comprised of primarily versus our legacy network.
That was the solution basically :3.