Q. There are three positions at a NGO that I am really interested in. The on-line application system allows me to upload a targeted version of my resume for each position. Is that a good idea or should I just use one resume for all three? A. I get this question a lot and there tends to be a deeper concern lying just below the surface. The worry seems to be “will I get found out for targeting my resume?” So let’s just get this out of the way. Targeting your resume is a smart strategy and a courtesy to the reader. You are simply highlighting your specific qualifications for a specific role. There is nothing suspicious about that.
So to answer you actual question, yes. Submit a targeted resume for each of the three positions.
Because it is likely that all three resumes will be read by the same people (just assume they will be), make sure the three resumes complement one another. Remember, targeting does not mean sweeping changes (or presenting dishonest content), it means subtle shifts to focus on different aspects of your expertise. That's why it's a smart move!