Do you want to get fancy and try to simulate sunrise and sunset? If so, I'd go 3x24" otherwhise I'd probably do 2x36". I suspect you'll find the bulb price for 24" vs 36" is about the same, so you'll save money on bulbs with fewer longer fixtures. I wouldn't do a single 4' light in a 6' tank unless you like shadows in the corner. If these are refit kits though I suppose you could stagger the two 48" bulbs such that they reach both ends and overlap in the middle? That would only work if you're willing to run the same bulb in each. Without knowing the respective costs of the fixtures and their bulbs though, it's hard to give an educated recommendation.
-Rick (the armchair aquarist, who assumes these are double-bulb refit kits?)