I'm currently trying to transfer everything into Capacities from Obsidian. I just do it as I need it at the moment. Anything I use in my workflow has to have a fairly specific purpose. So Zotero collects all references as big holding tank. It's pretty adaptable to work with writing software. Even though I can take notes in Zotero, I don't. In terms of reading papers, I'm a great fan of paper but to get a little more integrated I use my ReMarkable tablet. I'll then add in notes to the relevant places in Capacities; I used to use Obsidian for this. If I need to visualise something more organically, I used Scrintal, but my ReMarkable now fills that need. I do some writing in Capacities, but it's more focused on notes. I'm undecided as to my final thesis software; Overleaf, Word or Scrivener!