I was about to make a tutorial, but the process is so easy that you need no tutorial.
-Make a decent-poly cylinder(maybe around 30 sides) with a lot of height segments(the more segments you have, the better the final shape). Make the cylinder as long as the engineering section you want to build.
-When using the FFD modifiers, make sure after you selected an FFD Modifier, be sure to select "Control points." You can select individual points or whole rows of points to "mold" your shape.
-The FFD modifier I like to use is the FFD (box) modifier. By selecting the "Set Number of Points" button, you can change the number of points on the modifier- the more points, the more complex shape you can mold and stretch.
**Note- build every part of your starships in sections. This brief tutorial was on the "main" section of the engineering hull. The parts closer to the deflector can be built with additional cylinders.
Just play around and have fun.