I think the first step is always going to be to "define your rottenness", as it were. Truly rotten wood tends to crumble under pressure and has lost nearly all structural integrity and strength. You can saturate it with Git Rot, CPES or other diluted epoxy products and usually make it hard again, but you are not really going to make it strong again. The resulting piece will never have the same sort of strength or physical characteristics that it originally had. Whether or not you can get away with that depends on the spot in question and what sort of in-use stress it will get. If your particular "rot" is more a case of severe weathering, and/or maybe losing some of the original material, but decent structure remains, then you may still have sufficient strength left to live with and can augment it with your repair.
As a general rule of wooden boatbuilding though, it is always better to replace obviously bad wood with new wood whenever possible. If you have stuff in there which crumbles away when prodded, it is really difficult to make a good case for keeping it, and usually pretty foolish to think that the application of some form of modern goo is really going to fix it.