If you are starting a more "professional" academic journey, as a master or PhD student, I strongly recommend that you use a reference manager to help you organize and keep track of the things you read.
The two main roles of a reference manager are: a) help you organize papers and books you read and b) facilitate citation and referencing when producing your own text. The most common options I know are EndNote, Mendeley and Zotero. The first is paid and proprietary. The second is free (of charge) but not open source (although very friendly with users). The latter is free (of charge) and open source, so it is my choice!
Below, I will present basic steps to set up Zotero, recommend some good practices, offer some specific tips that are useful for me and, finally, make some comments on advanced features.
The only limitation that is worth mentioning is the fact that Zotero does not have a built-in pdf reader, as Mendeley (I do not know about EndNote). So, every time you open a PDF stored on your collection, Zotero launches the reader on your system and you have to make notes, highlightings and annotations in it. I actually prefer this way (I like my PDF reader - Okular), but some people may prefer a built-in reader to stay always inside the same environment.
Most of the info in this post is also on this pdf that I used in a presentation at the 2017 PGR Conference - School of Education, University of Nottingham. Feel free to use and distribute it :)
Before the instructions, some comments on the interface. On the left you have the organizational features: collections (similar to folders) and list of tags (on the bottom). On the middle you have your entries (each entry can have sub-items such as the actual pdf file, notes written on zotero, images, etc). On the right you can see the metadata of the entry selected in the middle column (basic info such as authors, title, journal, etc), notes (you can use this features to attach your comments on the entry for instance), tags and a list of related papers. Note that Zotero can fill the basic info for you, but the other tabs have to the generated by you.
The three ways to add a source are:
In terms of organization, I recommend to use lots of tags (easier to combine) and be more selective with the Collections. Finally, check regularly the “Duplicated Items” collection to avoid surprise in the future when writing.
This is a suggestion I read online a long time ago and found very useful during my PhD.
Zotero allows you to create collections and subcollections, which can be flexibly reorganized and renamed according to your wishes. My suggestions is: create a structure of collections that mimics the structure of your thesis. Of course you are going to change your mind during the process, but you can reorganize the collections as well to keep some resemblance.
I found this useful to recollect in the future, when you start to actually write up your thesis, the papers you read in the beginning of your research. So, when you get to your Methods section, let's say, you can check the references on your Methods collections. This way, you do not have to rely on your memory.
Zotero's Advanced Search is extremely powerful, allowing you to create searches combining collections, tags, search on all the fields of an entry with regular word searches. Also, it allows you to save the searches in case you want to use them in the future. This can be very powerful if well utilized.
Also, Zotero organizes the metadata in a readable and intelligible database. That is the part I love about open source! If you need to fiddle with the metadata in a way that is not supported by the software, you can open this file using any database tool and read it! And script it!