I find that Zettlr [ˈset·lər] and Zotero make my life easier. I have used it to make bibliographies with several papers now, all while keeping a digital Zettelkasten. It just requires knowledge of Markdown syntax and how to use Zettlr for note-taking. The best part is how easy it is.
You just need to download the extension for Zotero which is what you will be using to create citations – without having to install plugins on the website. You simply open Zotero, create a “Collection”, then you add references as you browse. If you go to a link in your browser and click the “Save to Zotero” button for the extension (it’s available for both Firefox and Chrome/Chromium browsers), you can save multiple references in your Collection. This allows you to, when done, simply export to a bibliography in various formats. It makes note-taking a breeze and it improves your ability to read without having to stop so often to manually write up your references and lookup things. There is a very handy setting in Zotero that allows to import all metadata for a certain DOI or arxiv number, just by pasting the number into the “Add Item(s) by Identifier” button. It pulls all the information for you in a second. No more manual references. The only thing is you will have to manually set the reference pointers like I have done in this post. Numbering and setting the #refs themselves is pretty easy, just create a numbered list in the markdown editor or your IDE.