The early missions, according to the film, were done in daylight and in formation. They planes flew at such a high altitude that the Japanese anti-aircraft shells could not reach them.
The problem with this for the planes, though, was that the winds at the altitude they flew at were strong and thus their bombing accuracy wasn't very good. According to some other sources I have read, these early missions were basically considered failures.
By the beginning of 1945 the raids were beginning to be a little more accurate and started doing some damage to the Japanese war machine.
The B-29's were so complicated and not totally tested out that mechanical failures cost more planes to be lost than did Japanese fighters and anti-aircraft, especially in the early phase of the bombing.
The entire bombing program was changed. The altitude was lowered, the planes flew at night, they did not use any specific formation, and they changed from almost all regular bombs to incendiary bombs. In the first night of bombing of Tokyo, 80,000 people were killed.
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