At the end of the alpha.txt file (if you're playing SMAC) or the alphax.txt file (if you're playing SMAX), there is a section #FACTIONS (for SMAC and SMAX) and #NEWFACTIONS (only for SMAX).
Find the name of the faction you've replaced, e.g. BELIEVE BELIEVE and replace with the name of the your file, e.g. YABURU YABURU (assuming you named the custom file YABURU and make sure the name of the file is YABURU.txt).
BTW, the forum Petek reference is a great resource for faction designers, mod creators and scenario designers. I'd encourage you to browse it; however, it may be less frustrating if you post your questions in THAT FORUM (I check there daily) and let one of those forum members answer your question or provide the appropriate link.
Another use of that forum, which I encourage, is to post your custom faction for comments.