It really depends on how much you concern yourself with repeatability. To Qhrumphf's point, it'll be hard to repeat your recipe exactly. OTOH, if you're like many of us, you just want to get a decent brew out of it. In that case you can split your boil and not worry too much about hops, water quantity, mixing etc...
I did split partial boils and just divided up the hops so that each pot would get the same %age approximately. I now have a 10 gallon kettle and I'm not happy with using the stovetop in full boils, it's way too slow.