If they're logged in, you can substitute the autogenerated client ID with your own user/account ID (make sure to anonymize it before sending it to Google).
With the Measurement Protocol it's the cid
parameter:
...v=1&tid=UA-XXXX-Y&cid=my-user-identifier&t=event...
In the Universal Analytics JS code, it would be something like this:
ga('create', 'UA-XXXX-Y', {
'clientId': 'my-user-identifier'
});
Hope this helps :)