Create separate config files for each device you want to monitor.
Then create a "master" mrtg config file that is nothing but global config entries, and
Include lines that point to each of the individual device config files.
I'd recommend, though, switching to using the RRD backend for MRTG, separating your "data collection" from "data display", and look into using something like
Routers2 to dynamically create the graphs as needed.
We do this, polling for network stats and load averages every 1 minute, disk I/O every 2 minutes, CPU stats, memory stats, and load averages every 5 minutes, and disk usage every 15 minutes.
For over 127 servers across the district. All nicely laid out in cascading menus by Routers2, with graphs only being created when viewed.