Enable On-Screen Btn and Disable hw Btn

First of all, root is required to edit these files.

Basically, all you have to enable the software buttons, is add 'qemu.hw.mainkeys=0' to the build.prop in /system and reboot.

Deactivate the hardware keys.
Go to /system/usr/keylayout and open 'Generic.kl' in a text editor and find the lines that say 'key 139 MENU WAKE_DROPPED', 'key 158 BACK WAKE_DROPPED', and 'key 172 HOME' and place a # at the start of each line like:
#139 MENU WAKE_DROPPED
#158 BACK WAKE_DROPPED
key 172 HOME (I would not recommend and disable home)

Take care here because if you add a # to the wrong line, you won

And last, navigate to system>usr>keylayout. We will be looking for a file called "sec_touchkey.kl".
Out the keys you don't want to work with a #.
So if you are like me and think the home button is fine, it will look like this.

#key 139 MENU
#key 158 BACK
key 102 HOME
key 217 SEARCH

UPDATE: For Customize Navbar Go to Settings-->Buttons

Just remember to remove the # - before you update the Cyanogenmod version to a newer.