Overlapping Regions Logic Pro – 3 ways to Deal with Overlapping Regions
Click on one of the overlapping regions in the Arrange Page to select it.
In the Arrange Page menu bar, click on Region>Remove overlaps
Overlapping Regions Logic Pro
The resulting overlap shortens the end point of the first region in the overlapping sequence, leaving the second region in tact.
With the track selected, in the Arrange Page menu, click Track>New for Overlapped Regions

Overlapping Regions Logic Pro
Once Step 1 is complete, Logic Pro creates a new track for overlapping regions, including any plug-ins and settings.
Overlapping Regions Logic Pro
(i) Press the ESC key on your QWERTY keyboard to select the Crossfade Tool
(ii) Using the Crossfade Tool, Click and drag over the area of the overlapping regions you wish to blend. The wider the crossfade you draw, the slower the blend.
Overlapping Regions Logic Pro
Step 2
The resulting crossfade draws a volume curve down from the first file and up from the second region, giving a smooth transition. This works well for eliminating clicks or obvious changes.
Overlapping Regions Logic Pro
Original source: http://www.logic-cafe.com/Article_View.asp?ID=163
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Another great way and probably the easiest out of them all is to
-Click on the drag menu in the arrange window
-Select & Click No Overlap
This will basically cut every region automatically when you have a region overlapping another.
Quick and easy!