Those are very good questions and quite tough to answer in a concise way. For me, it started with a book called Bad Science by Ben Goldacre who is a British medical doctor. Goldacre’s very good at breaking down the issues around poor reporting of science and health so it’s a great primer.
Once you learn how to spot the “red flags” it’s much easier to sift through the reams of information and drill down to the actual evidence.
Here’s a really good resource that has lots of information on understanding how to process claims and evidence:
This is a hub of resources and expertise to help you make sense of evidence.askforevidence.org
If you’re really motivated the best thing you can do is surround yourself with skeptical and critical thinking. Reading material is an obvious one, but there’s also podcasts to listen to, YouTube channels to follow, Facebook groups and pages, websites — pretty much whatever you’re into, you’ll find some skeptical resources.
It might seem daunting at first but once you start getting a feel for what’s generally reliable and what’s not, it gets a lot easier.
Facebook groups and pages are a great way to start because of the social nature — you can ask questions, see other people’s questions and engage with actual experts who can help you sift through. There is a group called Healthy Evidence that would probably be a good place to start.
You mention about doctors and scientists disagreeing. What you need to be careful of is that just because some members of that group disagree, that doesn’t mean there isn’t a consensus.
There are some climate scientists who don’t believe in human-caused climate change, for example, but 97% do, based on the evidence we have available. It’s also important to distinguish consensus between individuals from consensus of evidence — if you have 99 studies saying one thing, and one study saying another, it’s more likely that the 99 are correct and the one is an outlier.
Also just a word of caution — don’t get too hung up on natural vs synthetic. As long as there’s robust evidence for safety and efficacy, you can be confident regardless of a drug’s origin. Our bodies can’t tell the difference between natural and artificial versions of a compound- if they’re chemically identical, they will work the same way.
A properly-tested and regulated synthetic is probably safer and more effective overall than an untested and unregulated natural substance. Here’s a great article about some of the issues with natural remedy regulation that I think you’ll find useful:
If there is one aspect of "alternative" medicine that both critics and fans should agree on, it's that products should…sciencebasedmedicine.org
Hope that helps :)