I bred and hatched two Feebases. One has the nature Timid (which is decent, but not exactly what I want) but has good IVs, and the other has Bold (the desired nature) but has some pretty bad IVs.
Which one should I pick to add to my team?
I’d go for the IVs.
If you’re already breeding, you might as well breed to perfection. Get a 6IV ditto and keep going with the Bold. 
Holding an everstone passes on the nature.
If your still going further give the bold one an everstone and continue breeding but if your going to stop there I suggest going with the bold if you don’t want to deal with the PokéPon and give it IV Stones