You don't need to maintain two separate, identical sites, just the one you want to be the "real" site. Then log into the GoDaddy account for that domain and set the .com domain to forward to the .net domain (use unmasked forwarding). Now if someone types in .com they'll go to .net automatically and the URL in the address bar will be the .net one. This won't affect search engine rankings at all since there are no .com pages to index.