for me easiest way to do this was to get a good size tube and suck the gravel out thereby doing a wc at the same time worked like a charm no ill effect
You're best off doing 1/2 then the other half. Since you're losing the bacterial in the substrate, your filters will need a few days to catch up with the bioload. The larger the bioload of the tank, the smaller the amount of gravel you should remove at a time.
That being said, I've removed all gravel at once with no ill effects, but only on tanks that were running less than 1 in^2 of fish per gallon.