To distinguish between pitches, all you need is suffixes in the OTO. For the sake of organization, people often separate them into separate subfolders, but you could theoretically just dump all the audio in a single folder.
Let's say that you decide to use a standard CV reclist, and record into multiple folders. Here's what that would look like.
Code:
voicebank (folder)
readme.txt
character.txt
low (folder)
oto.ini
a.wav
ba.wav
... etc ...
zu.wav
high (folder)
oto.ini
a.wav
ba.wav
... etc ...
zu.wav
When you load the whole voicebank in UTAU and open the OTO, you'll be able to see all of the OTOs at once, but each folder will still have their own OTO.ini file. (This only applies to Windows. On Mac, using UTAU-Synth, there's only one oto_ini.txt for the whole voicebank which has entries for every folder.) Let's look at the OTO for the low pitch only.
Code:
a.wav=aL,0,0,0,0,0
a.wav=あL,0,0,0,0,0
... etc ...
zu.wav=zuL,0,0,0,0,0
zu.wav=ずL,0,0,0,0,0
The high pitch would look much the same, but with an H instead of an L. Suffixes don't need to be H and L, they could easily be the actual pitch being recorded (such as G3) or really anything you want. The important part is to distinguish between the pitches using unique suffixes. However, I would not recommend using special characters like kanji or unicode arrows. These can easily be mojibaked, so stick to things that are easy to type.
Every wav file needs to be duplicated in order to have both romaji and hiragana. The easiest way to do this is to OTO the bank entirely one way, then duplicate all the lines to add aliases for the other way, so that you don't need to OTO it twice. Alternatively, you can avoid having to make duplicate lines in the OTO by naming the files with suffixes in the first place. So if your file is "zuL.wav" you only need to have "ずL" in the OTO.
For UTAU to recognize which samples to use for which notes automatically, you need to set up a prefix map. This can be accessed from Tools > Edit prefix.map. Select all of the keys you want to use for a certain pitch, enter the suffix, and press "Set".
An example of a multipitch CV Japanese voicebank is KYE. You may want to use it for reference.
https://utaforum.net/showcase/kye.574/