It depends on your playstyle and needs. Also whether you mean "use the
Custom Stockpile choice in initially designation" (which I never do because...) or (... I instead am always) "designating, say, a Stone stockpile then immediately/later
recustomising additional classes of material into it".
In short, though, whichever way you do it you should avoid having "refuse" alongside food and/or clothes, but as an initial underground store to take everything from the wagon into safety it saves time. But you might want to exclude the "stone" class (as well as refuse) from this take-all stockpile, as gathering stones from your tunnels will doubtless distract the hauliers from bringing the food and anvil underground, etc.
If I
do make a master stockpile, though, I will also use it as a memorandum for what further stockpiles I create. Once I create a dedicated Food stockpile, Food will be removed from the "everything" pile (both to shift it and remind me), or if it's a seed stockpile, just the seeds, or if rock nuts get their own stockpile, I remove just
them (or remove them from the Seeds stockpile, having removed seeds from the Food stockpile, having removed that from the Everything stockpile, in a multi-tiered act of redelegation). I may have multiple stockpiles for something (e.g. multiple single-tile stockpiles for alcohol barrels, next to similarly multiple single ones for Prepared Foods, all taking from the respective master alcohol/PF tiles to put sustenance near to dwarves that might need them) but by that stage I am picky about mixing these end products in any coverall...
But that's a personal playing style.
The major disadvantage of a single (almost-)all-inclusive stockpile is, or at least was, job queueing issues. But when your workforce is limited this isn't always so obvious. If it saves you time designating, use Custom Stockpile (or customise a given base of stockpile to cover more bases) just to save you the worry. I still start off creating multiple 'strips' of stockpile, though,
even if they are initially all the same. Once I want to separate tradable crafts (crowns from sveotwrs from rings from earrings, etc), if I have seven or more different Finished Goods stockpiles, I can redifferentiate them down into one subtype each (at least, if not further splitting a larger multiple into quality/material differentiations, too) and wait for the hauliers to stockpile-shuffle them across as necessary, or with a forced dump/unforbid cycle to encourage this to happen.
But that gets into advanced technique (and personal preferences) territory....