No reason you can't equalize all at once as long as the charger
has the capacity to maintain the equalization
voltage on the full bank. Probably does, but if it is a tiny charger on a large bank then...
If doing the whole thing all at once will you have all your loads disconnected? Some loads may not like the 15+V used for equalization, and to be effective you really don't want loads to pull down the voltage. If you can't disconnect everything then charge 1/2 at a time, leaving your loads connected to the other bank.
Have you checked SG of the cells? Differing SG (when fully charged) is a good indication of required equalization.