Timing - controllers have clocks in front of them which show seconds so it's fairly straightforward to work out the separation.
Times are usually recorded using the 30 second point as the minute changeover. So if an aircraft takes off at 18:22:28 it's logged at 18:22. If it goes at 18:22:32 it's logged as 18:23. The timing for the log is at lift-off, not start of roll. However, for separation, timing usually starts at commencement of roll with appropriate allowance made for the type of the next a/c for vortex wake purposes.