If you make a marquee selection in the audio region, and then use the Gain tool, the change applies only to the selection, not the entire region.
In Logic Pro, select the Gain tool from the Tool menu in the Tracks area (or use the Gain Tool key command).
Do one of the following:
Hold the pointer over an audio region.
Make a marquee selection in an audio region.
To edit multiple audio regions, select the regions.
A yellow line appears in the region or regions, and the gain is displayed numerically in dB.
Drag the pointer vertically to increase or decrease the gain.
The numerical gain value updates as you drag.
Option-click the edited region or selection with the Gain tool.
Download the guides:
Logic Pro User Guide: PDF