I like zothero for managing the bibliography itself.
Comparing notes is hard and not super helpful to be honest.
What I would do:
- Bibliography in zothero, make sure it's in order and you tag/group things to have a good overview.
- Using something like a miro board or obsidian canvas or whatever you feel like to create a visual structure how paper relate to each other. This is super hard and takes a lot of time. I guess you will need to spend at least 6 months in the field to have an overview of what's happening and what has happened in the past and how everything relates.
- Create a mental model of the things you read. Not sure what field you are in, but in electromagnetic wave propagation and imaging, a lot of methods are very similar to each other. Additionally, a lot of these methods have been around in other field for a long time, too, likely named differently. So understanding the fundamental concepts of a paper is usually more important than understanding the details right out of the gate. That's why it is important to read a lot of papers in the beginning, too.
- Organize a paper discussion club in your group. Depending on how well-aligned your research topics are, it can be beneficial to talk about these papers. How did you understand it? How do others understand it? Different people have different interpretations and different mental models. This is a great way to learn more about your colleagues, see different perspectives and talking about papers is a great way to deepen the knowledge. Depending on the papers and how often it naturally occurs that you read the same papers, monthly or even bi-monthly meetings for this are probably enough but that's up to you.