Highlighters and post-its are useful friends - but when it comes to research papers, you are better served with a reference management tool. The programs support you in managing your own reference collections as well as in writing academic papers.
Useful Functions of Reference Management Software
Store reference and sources systematically
Structure notes and excerpts
Integrate citations easily into texts
Create a bibliography with one click
Thinking aids: create cross-references more quickly with an overview
What to Bear in Mind when Choosing a Software
What technical requirements do I need (operating system etc.)?
How intensively do I want to exchange information?