How to read and analyse a paper?

Hiya

I've recently started my PhD (NZ) and am flying ahead with my literature review / research proposal (thank god), but I'm sort of struggling on the reading side of things.

I'm wondering how you best critically analyse a paper?

Do you use a software to store comments that you generate from the paper? If so, what do you recommend?

How do you keep track of the papers you've critically read?

How do you remember the little tidbits from each paper that you can use to reference your text?

Still figuring the reading part all out so any advice appreciated!

TIA!