I have conducted a test, using a custom created bard/aa, and as far as I can tell, the bonuses apply regardless of where the arrows come from. My 30 aa/10 bard, with no buffs, using a non magical long, and a non magical long bow with unlimited lightning arrows had the exact same damage bonus, less the electrical damage from the unlimited arrows.

Aha! Nice to know! So if the AA uses regular arrows is the damage less or the same? This really helps as I was under the impression that magic arrows didnt get the bonuses before. :D

The enchant arrow feat gives you a bonus to hit and damage regardless of arrow type (or bow type for that matter). Magic arrows get the bonus too, but the better one applies. If you have Enchant III and a +4 arrow, the bonus is +4. If you have Enchant VI and a +4 arrow, the bonus is +6.
As long as your enchant level is higher than your arrow's own enchantment, and the arrows have no additional properties like elemental damage or poison, regular arrows are as good as magical ones.

It's the "Most favorable" thing. I've noticed that a lot with stuff in game, both in weapons, and armors. Stuff that won't stack will take the most favorable option. As Legolas pointed out, if the AA bonus is 4, but you're using a +6 arrow, then you will get the plus 6. Ideally, I'd like to have the +10, but.... [img]graemlins/heee.gif[/img]

Thanks guys! I'll try and remember that when I'm playing my AA's. :D