The best way to "learn" your network and how it all ties together is to manually draw it out (whether with paper and pencil or VISIO type drawings doesn't really matter).
There are tools that will do this automatically, they include CiscoWorks 2000, SolarWinds, What'sUp Gold, etc.
You'll want to include Layers 1 - 3 initially. Eventually as you understand how your network is layed out and what it's norms are, you want to include layer's 4 - 7.
I'm assuming you have access into the routers and switches, so start at your core or wherever your demarc starts with your ISP. Use CDP and telnet to work your way through your network.
