The passage in Genesis 1:1 is not referring to heaven in the sense of the dwelling place of God or the resting place of immortal souls. The hebrew word here is shamayim and it is more clearly defined as “firmament” which means ‘the vault or arch of the sky’. It refers to what we can see in the sky i.e. the dwelling place of the sun, the stars, the moon, the blue sky, etc. It’s for this reason that we often imagine heaven as a place that we go to up in the clouds, which is cute for cartoons but biblically unfounded when referring to life after death.
All that to say, the verse is not talking about multiple heavens, it is referring to the separation between the earth and what’s above the earth, i.e. everything.