Is there a way to make Arduino Mega run commands???

Working on a project where I need an Arduino mega (lots of digital and pwm pins), and a code I'm working on requires commands. Is there any way to get the code to work with the Mega, or will I have to get an Arduino Micro to run independently and split my code in two - one for the mega and one for the Arduino? I'm relatively new to Arduino, so a bit of guidance would be appreciated. We're running Arduino Mega2560 R3.

code I'm working on requires commands.

Are you desiring to interface the Arduino with a PC over USB HID?

To my knowledge, I have not seen a 2560 LUFA bootloader implementation nor a V-USB library for the 2560. Rancidbacon ported V-USB to the 328 as an Arduino library. Here are some of my projects:

Depending on what you plan to accomplish, you could use V-USB (HID 1.1), LUFA via the Leonardo/micro mini, or some custom solution.