Can IG-88B use a cannon on both attacks? or is it like the BTL title where the first attack has to be primary?

Yes.

And just incase the one word answer you where looking for should feel just a tad thin, the card just says "after you perform an attack that doesn't hit", it doesn't specify what kind of attack, so your weapon selection is irrelevant.

88B is just like Gunner, in that it doesn't care what kind of weapon attacks first.

You also don't have to shoot the same target.