Snap Column Borders feature in the Global Settings area makes it easy to align column borders with the columns that are in the sections directly above or directly below the column you are manipulating.

Snap Column Borders

Once inside the PDF Designer, toggle to the Global Settings tab from the far left side of the left panel. Shown below, this is the third tab from the top and looks like a gear. Click the white switch besides Snap Column Borders to On.

Now when you are dragging your column borders you will notice that the border will turn blue when you are aligned with a column border that is above or below it. You'll see a straight blue line running through both borders indicating that they are aligned.