like brewchez said, split everything equally, including your runnings from each phase of the mash, so that you get fairly equal gravities starting the boil. only really thick gravity boils get less hop utilization at a noticable level.
I have myself done split boils with two 16qt stockpots, recombined in the fermenter for all grain batches, because my ceramic top stove burners won't run anything larger than about a 13" diameter pot.
And you can easily water bath chill those smaller pots in the sink or tub in about 15-20 mins...so you don't have to get a chiller like you would in a full 6-gal single pot boil.
Primary: English Mild
On tap: Pale Ale, Lancelot's Wheat, English Brown Ale, Steam Beer, HoovNuts IPA
Bottled: MOAM, Braggot, Raspberry Melomel, Merlot, Apfelwein, Pyment, Sweet mead, Cabernet
Gal in 2009: 27, Gal in 2010: 34, Gal in 2011: 13, Gal in 2012: 10