If you reuse the bulkheads, make sure the gasket seal is fairly soft and flexible so it will seal. And make sure it goes on the side of the glass away from the threaded section.
If you want to seal over the bulkhead holes (why?) you can silicone a patch over the holes on the inside of the tank. That way the water pressure is pushing the glass patch down onto the hole, not trying to push it off (what it would be doing if you patch it from the outside). If the tank is glass, use a glass patch and silicone it in place. If your tank is acrylic, use a piece of acrylic and glue it in place with Weld-on glue for acrylic. DO NOT mix glass and acrylic. Silicone does not stick well to acrylic and weld-on glue has no affect on glass.