Multi pitch help!! D: D:

A side note: Remember to look at the prefixmap and make sure that you are enlisting the files either prefix or suffix. This is a huge part that could impact the pitches of your voicebank.

Go to Voice Config> open> click on the breath/sample oto (not in D4 nor E4, but outside of it) and see if it loads c:

That's odd, did you try to look at the oto and add the sounds from there? Like copying the sounds from the reclist, then adding .wav= after them? That may work, though, if it's not loading the folder, try taking your voicebank out of your voicebank directory and then load it outside of the directory. If that works, then simply put it back in after you close UTAU and boot it up again.
As long as you have the pitches planned out, you can work on the prefix map at anytime during the otoing process. Really, that depends on your work ethic I suppose? 

Go to Voice Config> open> click on the breath/sample oto (not in D4 nor E4, but outside of it) and see if it loads c:

Breath folder? And yes, there should be a oto besides the sample c: it shouldn't be a problem to make if it isn't there

wow so that's multipitch how dose the utau know which notes is which?