Atomos units can monitor and record the embedded digital audio from HDMI / SDI devices and the analogue audio inputs. It is not possible to vary the gain for the digital audio as this is embedded in the signal. You can usually adjust this from the camera, please see your camera manual for operational details.
To adjust the gain on the analogue input you need to bring up the audio settings panel (accessed from the home page by pressing the audio bars in the lower left hand corner). For Blade and Ninja2 users the audio gain controls are the + and - buttons adjacent to the analogue audio channels. For Shogun / Assassin / Flame / Inferno users, press the audio options button in the lower right hand side of the audio settings panel. Here you can adjust the left and right channel gain independently.
Figure 1 - Audio options page for Shogun, Assassin, Flame and Inferno series
Figure 2 - Gain control for Blade and Ninja2 series