New earth is the mainstream universe after crisis on infinite earths, and before flashpoint. Prime is earth is the mainstream universe after flashpoint. When the reboot first happened, there where many changes, but many of them have been reversed.

You can look at the tags you added, it's not that hard.

So new earth is really the main universe

NE was the main universe. PE is now the main universe as that is what is in current publication. However, what ever universe you prefer reading can be your “main” universe when it comes to personal preference. Read what you like.

I'm so confused