Follow this recipe:

1. first you do mutate_insert ...; say you add a Phe in this fashion
2. then you look for a Phe which is nearby
3. do move_zone and double-click the Calpha of that Phe
4. use the dials to move this Phe into the density where your new C-terminal Phe should go; when it's in place DO NOT HIT YES !!!
5. instead, use merge_atoms to copy the CURRENT coordinates of the MOVED Phe to those of the NEW Phe
6. after that, hit NO immediately, so as to cancel the move_zone
7. draw a new object (zone ; end) and voila !

You can use the same mechanism to add entire helices or strands at the C-terminus.

You could probably also use the BATON command to position the Calphas, then do lego_auto_mc and lego_auto_sc and, finally, lego_side_ch to get the correct rotamers.