The development of Systematic Review Software has reduced the value of citation management software. However, this software is essential if you're not able to use Systematic Review Software. There are several citation management tools, some free and some fee-based, to help facilitate reviewing and sharing notes on these articles. The two that function best are the desktop version of Endnote and Zotero. Other tools (Mendeley, Refworks, EndNote Web, Pages, etc.) have limitations. Librarians at the Biomedical Library can discuss with you the benefits of some common citation management tools.
Once your citations are gathered, your team will screen the results to exclude irrelevant citations. You'll use the inclusion/exclusion criteria you developed in your protocol to do this. Typically, the process starts with looking at citation Titles and Abstracts. Once you've excluded citations that obviously don't fit, you'll read the full text of every article and again use inclusion/exclusion criteria to remove irrelevant citations. After finishing the full text screen, you'll extract data.
The standard practice is for at least two members to screen every citation in every step (Title/Abstract Screening, Full Text Screening, and Data Extraction), and a third member is included to resolve disagreements. This process is deliberative and painstaking by design. If only one person makes the decision about what is included/excluded, bias is introduced into the review. This process is one of the fundamental elements that sets systematic reviews apart from other literature reviews.
Fee-based tools such as Covidence or Rayyan can be valuable in the screening process, but the process can be conducted using tools such as Zotero and Excel as well. When using tools not specifically designed for systematic reviews, pay attention to version control and designate one member of the team to maintain backup versions of every element (citation files, spreadsheets, search strategies, etc.).