Craig,
Which graphics cards/processors are used depends on your system preference choice in the "Energy Saver". The computer will switch automatically, but may require you to log out/log in.
When you choose "Better Battery Life" then the Intel graphics processor will be used. Use only the laptop display with this setting and profile accordingly with your profiling gear. This selection is used when you're not using AC power.
When you choose "Higher Performance" then the computer will automatically switch to the AMD processor. This is used when AC power is available. You will want to profile the laptop monitor under this condition as well.
To use your NEC monitor, you will use the Thunderbolt port with the appropriate cable adapter (DVI, Mini-display port). The Thunderbolt/DVI adapter is optional, but I don't see it on the Apple web site.
Once your NEC monitor is up and recognized by the system, open system preferences and configure your dual-monitor set up (mirror, positioning, etc.). After that, run your display profiling software/hardware and you should be good to go.