Historically, the djinkim was present to denote either a glottal stop (hamza), and its ue was much less, mostly with ⲙ, ⲛ. However, as Coptic started to fade out extra djinkims were added to esp. at a string of two or more consonants starting a word eg ⲡϭⲟⲓⲥ, ⲥϧⲁⲓ,ⲥⲁⲣⲝ, ⲥⲧⲣⲁⲧⲓⲁ, ⲥⲙⲟⲩ, ⲡⲥⲟⲗⲥⲉⲗ, ⲥⲧⲁⲩⲣⲟⲥ, ⲉⲕⲕⲗⲏⲥⲓⲁ which when not used lead to pronunciations as setratia (instead of stratia), or sareks (instead of sarks). At other times, it was added automatically to any strings of consonants leading to akekisia (instead of eklisia).
Later, with Greco-Bohairic (GB) pronunciation, it became also a marker of accent like Greek language & French, and it was used to denote the extra glottal stops added by GB, in addition to the added djinkim infront of any strings of consonants.
Generally, I would not use it over vowels, never over ⲝ, ϭ, ⲯ, ⲃ, ⲅ, ⲇ, ⲍ, ⲗ, ϧ, ϫ, ϯ, only when a glottal stop is needed