I ni ce, @ni_pu !
The spelling variants all revolve around the use of different kanmasere diacritics, which can mark both vowel length and tone in N’ko orthography. In the cases that you list, the differences are all tonal.
In the cases, that you listed (e.g., the words for Ala, su, and hɛrɛ/hɛɛrɛ), there isn’t one single correct way to write the words because the two variants that you listed for each are a question of whether the word carries the floating tone definite article or not. That is, the choice between ߛߎ߫ {sú} and ߛߎ {sú ̀} (and all the other examples) depends on the specific sentence , the context and possiby what the speaker/writer wants to express.
For more about the use of kanmasere and tone in Manding and in N’ko orthography, you can consult the section “Pan-African Tones” in my dissertation (starting on p. 135), which is open-access here.
In the case of your example, I did some digging into the Maninka Reference Corpus regarding the common spelling of {Ala ye}:
So the most typical way (and arguably therefore the correct) spelling for a benediction would be:
ߊߟߊ߫ ߦߋ߫
From there, it’s not 100% clear. There are no benedictions that use {Ala ye su hɛrɛ siyaya} in the N’ko corpus that I can find. It’s not a common turn of phrase in N’ko writings or circles. (Indeed, it’s not the most typical night time benediction in spoken Maninka, which is often the source for many N’ko written conventions.)
There are two benedictions that use {Ala ye hɛrɛ …} though. In this case, one is with ߤߙߍ߫ {hɛ́rɛ} and one is with ߤߙߍ {hɛ́rɛ ̀}.
So, no definitive answer, but if it were me and I wanted to interpret the Bambara phrase Ala ka su hɛɛrɛ caya into writtne N’ko, I would probably write the following 
ߊߟߊ߫ ߦߋ߫ ߛߎ ߤߙߍ ߛߌߦߊߦߊ߫