If the bolt is broken off flush with the engine block, there's no sense in removing the manifold. However, if there is a stub sufficient enough to grasp with vise-grip pliers, then remove the manifold, soak it with Liquid Wrench, or Kroil for a couple days, then heat the block with a a propane torch. When the block around the bolt is fairly hot, grasp the bolt stub with the vise-grips and carefully work it back and forth until it loosens. This sometimes works well, and sometimes the bolt will break right at the block.
If that happens, the next step requires drilling the center of the bolt with a drill-bit that's slightly smaller than the bolt diameter. This takes a steady hand so you don't get off center. Once the bolt has a nice, clean, relatively deep hole in the center then you can insert an easy out. However, I would recommend again heating the block with a propane torch--this can make a world of difference.
Most of the bolts used in the Atomic-4 were mild steel, so they should drill fairly easily. Once the bolt is removed, it's a good idea to chase the threads with the same size tap that was originally used to tap the block. Before inserting the new bolt, you may want to use a good quality, thread lubricant on the bolt so you don't have the same problem in the future. And, if you have to remove the manifold, replace all the old bolts with new ones that are also lubricated as well.