It really depends on how you read the spell.
You can make the sphere [travel up to 30 feet per round and strike a creature or object you indicate as a ranged touch attack].
In this reading, the sphere is making the touch attack, so it does not benefit from your invisibility.
You can [make the sphere travel up to 30 feet per round] and [strike a creature or object you indicate as a ranged touch attack].
In this reading, you have two abilities - to make the sphere travel, and to strike with the sphere. Your invisibility would apply, since you are making the attack.
Since the sphere doesn't have any stats to make an attack, I would lean towards the second reading, but it doesn't make much sense either. What does "indicate as a ranged touch attack" mean?
However, Complete Arcane's version of the spell says:
It flies at up to 30 feet per round and attacks the creature or object you indicate. You must succeed at a ranged touch attack to strike a creature with the sphere.
This makes more sense, and carries the intent of the spell. You make a ranged touch attack to tell the sphere "this is who you go and hit" and then the sphere goes and hits it, no attack roll needed. Since you are the one making the attack roll, the target is flat-footed against you. Imagine shooting an invisible homing beacon at the target, who is too busy guarding against the magic flying orb to notice that you're aiming at it too.