It's all up to you really. You could just use a small amount (say about a cup) right in the wash cycle when stripping. Or you could also soak your diapers for a few hours in a high vinegar concentration (we're talking several cups here or even just the whole bottle if you're so inclined). The acidity will help dislodge the build-up more quickly so it should reduce the number of cycles you'll have to do.
There's no real right or wrong way to strip diapers or use vinegar during a strip. The basics are lots of very hot water (the hotter the better) 'washes', no detergent and use vinegar essentially as desired.