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
- 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
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.