To reverse the faces of the bolt heads. Pick the top face of a bolt - right click - Select > All Connected. Right click again, while over the bolt head - Reverse Faces. That's the easy part.
The main problem with the model is you have faces on top of faces. That is why you are getting faces in the wrong direction. Which confuses the software into not knowing what is inside and what is out. Every time you draw a line on a face an extra face may be created which will be on top of the original face. You need to be very careful when drawing lines to make faces, that they are joined at the correct 'end point ' for example. If the face does not appear automatically when you close a shape, do not just draw another line. Find out why the face was not created, by checking the end points of the lines.
You need to delete all of the extra lines you do not want. If you end up deleting the wrong line a face will disappear, just redraw that line. Some of the lines will be invisible. Go to - View - Hidden Geometry to show them.
Another thing you need to do when drawing is once you have drawn a shape, say a bolt head, select it and use the command, Right click - Intersect Faces - with Model or Selection , depending what you are doing. Then all of the extra lines and faces that are not needed can be deleted.
What you are really aiming for is one outside shell with no internal walls or faces. Be methodical as you draw. It may take longer but you will have less problems if you do it as you go along.