Hello I recently read the difference between the kun or on readings and understood it, now I know in which cases to use one or the other reading, but I still have a question. For example: the kanji 日 have 2 on readings - にち and じつ(and also two kun reading), then which readings should I use? How do I know which and when I have to use?
You should learn correct reading for each word. In relatively small number of cases, multiple readings of given word are possible.
Kanji 日 has also reading に often used in 日本 ("Japan") and its compounds: 日本語 ("Japanese language"), 日本人 ("Japanese person") etc.
All on readings of kanji 日 come from Middle Chinese *nyit, so /t/ in Early Middle Japanese forms of these readings (nit, zit) is regularly expected. ni developed as irregular shortening of nit.
Middle Japanese and Early Modern Japanese is known to have had syllable-final /t/ in Sino-Japanese vocabulary, so despite hiragana/katakana spelling of these readings there was no vowel after /t/.