Add minor OS X update to existing El Capitan bootable Install USB
The probably easiest solution is to simply download the latest OS X El Capitan installer after a minor update was released. Usually the newest installer available in the App Store already includes the update. 

To get the build version of the OS installed by the OS X installer.app enter in Terminal.app:

cat /Applications/Install\ OS\ X\ El\ Capitan.app/Contents/Info.plist | grep -A 1 BuildMachineOSBuild


The output


15A... usually indicates a 10.11.0 build
15B... usually indicates a 10.11.1 build
15C... usually indicates a 10.11.2 build


and so on. The build version here is not identical with the build version of the later installed operating system. To get that one you have to mount the InstallESD.dmg in "/Applications/Install OS X El Capitan.app/Contents/SharedSupport/". Then cd to "/Volumes/OS X Install ESD" and enter "open BaseSystem.dmg".

To get the Build or System version then enter:

cat /Volumes/OS\ X\ Base\ System/System/Library/CoreServices/SystemVersion.plist | grep -A 1 ProductBuildVersion


or 

cat /Volumes/OS\ X\ Base\ System/System/Library/CoreServices/SystemVersion.plist | grep -A 1 ProductVersion


With the new OS X installer you can create a new bootable USB.

Depending on your internet connection that's probably faster and less hassle/error-prone than merging an update in an older full installer.