The biggest difference I find is that with an inline varnish it will soak into the ink somewhat so you won't get quite as high of a gloss or quite as dull of a dull than if you ran it offline after the ink had time to dry.
Another factor might be the drying time. With an inline varnish you won't be able to back up the job right away and might have to pull the job rather than just throw a varnish on it the next day.
There have been jobs that I've run the first side without varnish and the second side with an inline varnish and just put the varnish on the other side the next day. This would only work if there was little ink coverage because of the visual difference I stated above, but it might help if time is a factor.
As far as tips on running it.......Overprint varnish is designed to do just that......overprint. It's already been adjusted to be last down so there's nothing to do to any of your inks unless you have one that is a very low tack.
Just don't makeready with your varnish on. Wait until you're ready to go and then make sure you have plenty of varnish on the rollers or it will tack up and you'll pull the colors you're overprinting into the varnish. You can usually run the same amount of varnish as you do when you run it offline.
Hope this helps,
Dave