How do I Make an upgrades system?

What it says on the tin.

I plan to have a system where players collect cash in game and then use it to buy weapons/ buffs

that automatically are on the player at the start of the next level.

Kind of a broad question. Lots of ways to do that.

Maybe make an invisible layer or another layout with the "shop" on it.

You'll probably use an array to store all the items.

Have some instance variables on the player that get set when they buy stuff.

Use those variables to set what the weapons/buffs do.

There's a shop tutorial. It's a bit dated, but still might help ya out.

Try it, then come back and ask more specific questions.