If there is excess liquid, place the mixture in a colander and squeeze out the excess liquid. So make sure the mixture is completely cooled, otherwise it's going to make the phyllo dough soggy, and you don't want soggy spanakopita. In a medium bowl, beat the eggs with feta and nutmeg then add this to the spinach mixture and mix until it's all incorporated well together.
So first thing first, we have to assemble the filling. By the way if your phyllo pastry was in the freezer, take it out in time for it to defrost. In a large skillet heat the olive oil on medium heat. Add the onions and saute until soft. Add the spinach and salt and pepper and saute until the spinach is limp. Add the lemon juice, and remove off the heat. Let cool.