We do something like what Dravot said. Enhancement bonuses have 4 effects: attack bonus, damage bonus, bypass DR, sunder. So, let the enhancement bonus of the bow contribute to attack bonus and sunder, and the enhancement of arrows do damage bonus and DR.
If you don't want to change things so fundamental, just say that this is how GMW works, that for ranged weapons you must enchant a bow AND 50 arrows with it when you cast, and the spell splits the enchantment itself.
There were three other possibilities given on the House Rule board that I liked:
1> When enchanting 50 arrows, the duration drops to 1 minute/level instead of 1 hour/level since you're splitting the enchantment up. So, if you want to GMW right before combat no problem, but it won't be the "enchant 50 arrows at the start of the day and split them up so everyone gets a dozen" situation it is now.
2> GMW increases the Enhancement bonus until the total Market Price of the item is +1/3 levels. So, casting it on a +1 Keen Vorpal Flaming Burst weapon does nothing.
3> Non-masterwork items can't hold an Enhancement bonus, so unless the arrows are masterwork, no such luck.
But, any "how would you house-rule GMW?" discussion should go in the correct forum. Not that there aren't a few billion threads on it already.