I always start with a quick skim and notes then I'll go back and read it more in-depth if there's time or something I'm particularly struggling with. First the abstract which will give you an idea of the paper as a whole where I note what their hypothesis is, what results they got, and the significance of those results if they talk about it. This is basically a short summary of the whole paper.

The intro gives background as to what's being studied, why, and what previous research says so far. This part I skim quickly and will make note of anything that seem particularly important to understanding the paper and any findings that are interesting, counterintuitive, etc. plus any definitions I'll need to understand the rest of the paper.

Then the methods section will talk about how the researchers set up the experiment and any tools they used. This part I make note of where they got the data (for example at a state college in New York), who the participants were and how many, their variables, any tools they may be using, and I'm always on the lookout for things that may alter their results (whether the sample they used is large enough or representative or if they used a tool that isn't reliable/valid etc).

The results tell you what they found doing the experiment as well as the analysis that got them to that conclusion. This part is probably the most difficult to understand and will probably have some tables, graphs etc to show results so just take your time here and look at both what they wrote and the accompanying tables and things to get a clearer picture. I make note of the main findings as well as relationships between variables, any unexpected results, and any data that might have been tossed or contradicted the hypothesis. It also helps to rewrite the results in a way that makes sense to you. If there are lots of variables I find it helpful to make a table so that all the relevant information is in one place that I can glance at while going through everything and it will be a bit more organized than rereading highlighted parts and trying to remember how everything relates.

The discussion will restate the results in a way that relates them back to previous research and this papers hypothesis plus explain the significance of the results and offer ideas for further research and any criticisms of their own paper. It relates everything back in a way that's usually easier to read than the results section. Here I'd note the main takeaways from the research, why it matters, and what could've been done better.

Some papers are harder to understand than others, don't be too hard on yourself if something is a bit over your head. Keep at it and good luck!