The Bombs Note is on a table to the left in the side room off the nave of Bill's church. Go into the room on the right, the one Bill makes clear is not the confessional.
Runners set off most of the bombs on the south side of town, so Bill needs another pass to replace them, and he reminds himself in capitals to mark every bomb on his map.
The church is where Bill and his partner set up their fortified home and built nail bombs, so this note sits right at the heart of his operation.
Bill's Map
Bill's Map is Bill's hand-annotated map of Lincoln, on a table with an engine near the door you come in through at his safehouse, right after you meet him.
Boy's Diary
The Boy's Diary is on the windowsill of a child's bedroom painted with stripes and cars, upstairs in the second house with the dry pool in the new territory beyond the church graveyard.
Fences Note
The Fences Note is another of Bill's reminders, on the table in the back room of his safehouse near the pipe he handcuffs Ellie to.
Hunters Note
The Hunters Note is a reminder Bill left on a table in the room at the end of the hall upstairs. Leave his safehouse, go up the stairs, turn right and walk to the last room.