Afloat OS X 10.11 (El Capitan) : Keep Windows on Top

Download SIMBL, at least version 0.9.9.
Open command prompt aka Terminal Window
Run following commands on terminal to install SIMBL-0.9.9 at /System/Library/ScriptingAdditions/

sudo installer –verbose –pkg Downloads/SIMBL–0.9.9/SIMBL–0.9.9.pkg –target /

sudo rm –rf /System/Library/ScriptingAdditions/SIMBL.osax

sudo mv /Library/ScriptingAdditions/SIMBL.osax /System/Library/ScriptingAdditions/

sudo cp –p /System/Library/ScriptingAdditions/SIMBL.osax/Contents/Resources/SIMBL\ Agent.app/Contents/Resources/net.culater.SIMBL.Agent.plist /System/Library/LaunchAgents/

sudo sed –e “s/Library/System\/Library/” –i “” /System/Library/LaunchAgents/net.culater.SIMBL.Agent.plist
Head over to https://github.com/vjt/afloat/releases/tag/v2.4.1 and download “Afloat-2.4.110.9x86-64.bundle.zip”.
Unzip the downloaded file to get “Afloat.bundle” file.
Move Afloat.bundle file to /Library/Application Support/SIMBL/Plugins
Restart OS X