I haven't read those comics, but from what a friend has told me there was a multiverse pileup. Each Spider is from their own universe - for example Peter Parker is from the 'normal' Marvel universe, but Miles Morales was the Spiderman in the Ultimates universe - but when the multiverse crash happened the Spider Totem (not sure what that is) pulled all of the Spiders out of the wreckage and they ended up in one place. Which confused the heck out of them all.
I think in the Ultimates universe Peter Parker lived there and took Miles as apprentice when he was exposed to the same stuff he was? And then Parker got murdered by one of his many enemies, so Miles took up the job full time.