Three quarters of the way back

Solution 1:

It means roughly three-quarters of the way back from the front row of pews. If there were 12 rows of pews they would be sitting somewhere in rows 8 to 10. The term "the middle pews" is most likely to mean the central bank of pews between two aisles, the other banks being the "left and right" or "north and south" pews.

Solution 2:

The use of a semicolon is strange—since what follows is not an independent clause. It should be a comma instead.

However, on Sunday mornings also doesn't belong—unless a comma is placed before it as well or some kind of conjunction is used with the comma after pews.

The least amount of editing would be:

This group [is] neatly tucked in the middle pews, three-quarters of the way back, on Sunday mornings.

Although it's not made explicitly clear, three-quarters of the way back is most likely referring to their position among all of the pews in general. So, while they are sitting in the middle pews, they are also sitting among the third quarter of pews.

Graphically, it would probably look something like this:

O O O O - First quarter of pews.
O O O O - Second quarter of pews.
O X X O - Third quarter of pews, in the middle, where the group is sitting.
O O O O - Last quarter of pews.