First, let me reassure you. If you're locked out or you don't like the changes you've made you can reset all settings by visiting the failsafe url that looks something like this@
You will find this link on the WP hide/Admin section. It will also be emailed to you at your default email address.
Secondly, what works best is to make changes one item at a time then check how that affects your current setup. Your personal theme and plugins may not all play nice together.
WP Hide/General/Html is where you can compress your source code making it harder to the average user to see what you're using. Test the option that works best for you.
WP Hide/Rewrite is the section where you really hide your Wordpress. WP Hide/Rewrite/WP Content enables you to change your /wp-content/ directory to something like /apps/ and at WP Hide/Rewrite/WP includes you cange your /wp-includes/ directory to /inc/
You will need patience and trial and error to find the option that works for you. You try the aggressive approach and activate everything at once and if that works for you then you're sorted!
All the best.