You need SNMP setup on routers and switches to read their topology and if you are actually doing networking you should be able to SSH into each device and add SNMP or determine the existing SNMP settings. How many switches routers and firewalls are in the network?
BE CAREFUL. The dude could peg the CPU on routers when it reads the settings from them. If the router is connected to the internet and using BGP the dude will download the entire BGP routing table. Care should be taken in setting up SNMP on the internet routers so that BGP will not be sent to SNMP.
To map layer 3 figure out your default gateway, that is a router. Manually add that as a device in the dude, that is your access router, if your network is laid out enterprise style you have core, distribution, and access devices. Use trace route to
www.google.com. Each HOP is another router but you are only interested in routers on the inside of your network. You can't and shouldn't attempt to monitor routers that do not belong to your company. That is one route in your network and can make a layer 3 map out of that.
You can log into a router and print the routing table, or if SNMP is working you can look at the router in the dude and see the routing table. You can decipher your network with the routing table but that is not something you could do with out knowing layer 3. "Show IP route" (CISCO) Will show you every route, many of those are point to point and many of those will be access networks. The point to point routes are distribution and the last hop before you get to the internet would be the core.
No one knows how much you know about networking. Do you know what layer 2 and layer 3 are? If not you need to learn that to build maps that make sense. Like the previous poster said most networks deserve two maps one showing physical (layer 2) and one showing routes (layer 3). To map layer 2 you have to log into devices and see what shows up using the tools built into that device. For Cisco you can type "Show CDP Neighbor" that gives you the names of any device running CDP (Cisco Discovery Protocol) and the port it is connected to. If your entire network is made out of Cisco devices you could map layer 2 manually. I would do it manually since you could affect the network by scanning it.
To use the dude to map the networks, Use the top map as a dash, add a submap for each location/subnet on the dash, inside each submap set the auto-discover range to the subnet the map represents. You do not have to use auto-discover and manually building maps is more accurate, but use auto-discover once then delete the stuff you don't care about and manually add links that make up your connections.
i.e. location 1 submap is subnet 6 which is address 192.168.6.0/24. or 192.168.6.0 through 192.168.6.254.
i.e. location 2 submap subnet 7 which is address 192.168.7.0/24. or 192.168.6.0 through 192.168.6.254.
On the dash connect the submaps with links to show how the subnets/locations connect.
Lebowski