If your empire is *really* big so that it actually spans multiple galaxies, you might want to base the standard clock on the cosmic microwave background. 

See for example [physics stackexchange][1]


  [1]: https://physics.stackexchange.com/questions/25928/is-the-cmb-rest-frame-special-where-does-it-come-from

Having chosen a standard clock, obviously you must then set a base time. As a galaxy spanning civilisation, you should have the technology to be able to use the start of the universe for that!

Alternatively, a civilisation with FTL would likely use that technology to manage clocks. Special relativity considers how light signals are passed between observers to come to its conclusions regarding clocks. So it will depend on how break the law of the speed of light being limiting that will determine how to sychronise clocks.