In many cases, I think it is a mistake to do a 6 yr ortho residency. My feeling is that many programs set up this extra year of research to bolster their own research program...it's a way for attendings to publish more with less work, and to foster more of an "academic" environment. Of course the focus is also on education, but I think in most cases this is a secondary goal. So the 6 year idea is great for the program and the faculty, but does not serve the resident who does this extra year well.
If you're interested in academics, your best bet is to do a 2 year fellowship in your area of interest, with one of those years devoted to full-time research. Keep in mind that an extra year of research is primarily geared for CAREER ADVANCEMENT. Many 6 year residencies have this extra year at the end of PGY2 year or some even do this extra year right after internship. This is a waste of time because at that level, you really don't know what area you will pursue, nor do you have the experience and are not yet "seasoned" enough as an orthopaedic surgeon to fully take advantage of this year of research. Of course you learn plenty that year and it may be a great experience, but if your goal is to be an academician, you get more bang for your buck if you wait until you decide what field you want to pursue, and then do a year of research either before or after your fellowship in that particular area at a high-powered academic institution like Mayo and the like. This is your best option and the best way to get your foot in the door in the academic world. You will be more efficient and will publish more at that level in your training as well. This also allows you to build a strong network in your particular area of interest with influential players who are leaders in their specialty. It makes little sense to do hand research for example, if you end up going into joints or spine.
Again, the purpose of the extra year of research is career advancement. If you're not interested in academics, you're wasting your time with a 6 year program.
These are just my thoughts. I personally would discourage anyone from doing a 6 year residency. I think it's a system set up to benefit the program and faculty, not the resident. Your best option is to do this year of research as a fellow.