Unless you want to make the highly disingenuous argument that Aqueous Orb doesn't specifically say it must move along the ground, there's no good option to make it fly. I guess you could try using something like Gravity Sphere, but it seems to me you'd be better off just doing something else rather than spending previous combat rounds and spell slots trying to force Aqueous Orb to work in a situation where it wouldn't normally.
If gust of wind weren't terrible I'd recommend that, but I think it unlikely your primary flying foe is faeries or something... so no idea.
This is why you want to be careful about what spell you perfect. Most spells have limitations, but aqueous orbs' limitations are going to come up more at higher levels. It's not just flyers either - teleporters can get out relatively easily.
Battering blast? Resistance or immunity to force is rare. Acid arrow has no SR and keeps on damaging the enemy, burning gaze is a spell you can share with your familiar to have them spend actions targeting it. Pellet blast has no SR and affects an area, and DR sufficient to negate all or the damage is rare. Swarm of fangs might work, ask your GM before committing to it.