/usr/local has been both re-creatable and writable on El Capitan since 2015-10-21 when Apple released
/System/Library/Sandbox/Compatibility.bundle version 12 in software update 031-40358 patching 10.11 and 10.11.1, and installed as part of the 10.11.2 update, 10.11.2 combo update, and 10.11.2 clean installs. You do not need to do anything special unless you have not updated to the latest point release of El Capitan.
A patched system will have compatibility bundle greater than or equal to 12 and show
iMac-TMP:~ joe$ grep /usr/local /System/Library/Sandbox/rootless.conf
iMac-TMP:~ joe$ grep /usr/local /System/Library/Sandbox/Compatibility.bundle/Contents/Resources/paths
iMac-TMP:~ joe$ defaults read /System/Library/Sandbox/Compatibility.bundle/Contents/Info.plist CFBundleVersion
An unpatched system will have compatibility bundle less than 12.0 and not have the
/usr/local entry in