An archer cannot put more than one slot in a melee weapon, thus they could only put the one slot into shortswords. I personally have never noticed much difference between being proficient and non-proficient in a weapon (-1 to hit and damage, but no loss of attack rate). Thus, put the five slots into longbow, then build up shortbows as backup weapons, due to the unlimited magic ammo shortbows out there. Use the longbows for most opponents, then use the shortbows for those needing higher level weapon bonuses to hit. Also remember that even though it is not your specialty, you can wade into melee, so you can use weapons like the Flail of Ages to handle opponents you can't hit (yes, it is the equivalent of +2 in nonproficient hands, but the energy damage more than makes up for it). Finally, against tougher opponents or stoneskinned mages, use energy arrows, especially acid arrows (since they require no save). I tore up Firkragg with acid arrows (he was actually pretty easy once I used items to get fire resistance above 100%
).
In other words, be versatile. Just because you are not proficient in a weapon, doesn't mean you can't use it. And if you can't hurt the opponent with the weapon you are using, switch weapons. Always alter your tactics to fit the battle at hand, otherwise you will have problems, regardless of what class you play.