Film: This is something that's completely omitted from the film. We don't know where It comes from. We do know that It's been around for decades, but that's about all we get. Though we see It's lair, we don't get to go inside and see how It came to be and where It truly dwells.
Novel: It's origin is a huge discovery during the Losers' time as kids. One day, they build a makeshift American-Indian smokehole, which was supposedly an ancient way of having visions. Richie and Mike vividly hallucinate and see It's origin, which stretches back centuries, possibly millennia. It has always been here. It first awoke when mankind arrived.
Here's another wild thing that's been left out. There's only one place the Losers, specifically Bill, can actually defeat It, and that's in a place known as the Macroverse. This is somewhere in another dimension, a sort of psychic arena where Bill can face the spirit one-on-one. Luckily for us, director Any Muschietti said he will introduce this aspect in the sequel.
