First start off by loading your body, I will use the small cylinder so show how it's done.

As you can see I made the cylinder and everything is ready to go.

Now in the next image you can see that I've selected the top of the cylinder. Once you've selected the top then click vertex and remove the surface from the selected area.

Now that you've removed the poly's from the selected area it should look like the image below.

Now that you've cut off the top you need to create the circle of the desired size you want the cockpit to be.

Once you've done that you need to move the circle above the cylinder like I've done below

Once you've move it where it needs to be, then you need to select the area you deleted and the new circle you've just made.
It should look like the below image.

Once you've selected the area, then go to vertex at the top and click create surface.

When you've done that your body should look like the image below.

 

Once you've done that you need to clean of the stuff you just made. Select all the parts you don't need. Like the circle and the front parts of the cylinder and also the flat line down the middle, it will be on the selected line you see below.

Once you've done that all you need to do now is move the new hole down to be level with your body.

Then just move the vertices around till they are rounded with the body.

 

Congratulations! you now have a nice hole in your body to place a cockpit. Enjoy!