How do you store freshly pumped milk...

In storage bags? I feel like I’m doing it wrong. I have a few frozen bags but I feel like it’s not right. When I pump, I put the milk in the bag; I try to get air out, but when I lay it flat I see bubbles? And I put it in the freezer not on top of each other and when I went to put the frozen ones in a box it had the lines from the freezer shelves (I forgot the name lol). Will the bubbles ruin the milk? And will the indents ruin the milk?

What do you do with your freshly pumped milk and storage bags?

I’ve been using bottles the whole time until I ran out of the ones the hospital gave me while I was in there.