I was diagnosed with keratoconus in one eye & given a scleral contact for that eye only last week. why when i wear the lens, i can see out of each eye individually but when looking through both eyes together, i feel cross-eyed & my vision is blurry?

A keratoconus (KC) eye is likely to be very myopic compared to a non-involved fellow eye. So the corrective lens, which allows good vision, produces an image too different in size from that of the other eye to see clearly with both eyes together. Your best bet is to seek an ophthalmolgic specialist termed corneal specialist to work on this problem.