I'm super confused about Dayaj'a'. Sometimes it means do you understand and sometimes did ge/she/it understand
Dayaj'a' should never mean, "Did he/she/it understand?". The prefix Da- means that the grammatical subject (the person/thing doing the action) must be second person singular ("you") and the grammatical object (the person/thing the action is done to) is third person ("he/she/it/they"). To get "Did he/she/it understand?" you would need to have a null prefix (the absence of a prefix really, but for consistency in talking about prefixes I prefer to treat it as a silent and invisible prefix) which would give us yaj'a'. Note that your other suggestion "Do you understand?" has a second person subject ("you"), but doesn't have an object at all. This would be represented by the prefix bI- as in bIyaj'a'.
An explanation is given in the Tips & Notes, but I know it’s a lot of new information and some details are bound to be difficult to understand or slip through the memory. However, since Duolingo has hidden the Tips & Notes I want to make sure you know about them and where to find them. If you have not been reading the Tips & Notes, I would like to ask that you review those so we don’t have to repeat too much of the information that we have explained there.
If you are doing the course on iOS or Android, you cannot currently access the Tips & Notes through the app. To access the Tips & Notes, you will have to access the course using a web browser at https://www.duolingo.com/. You can still do it on your mobile device, but you will have to use the web browser instead of the app (or you can do it from a computer). When you click on a Skill, it will expand to reveal a Start button, a key, and a light bulb.
If you click on the light bulb it will reveal the Tips & Notes and give you a detailed explanation of the grammar that is introduced in that Skill. If you have questions after reading the Tips & Notes for any Skills, then please return to the forum to ask your question, explaining what you didn’t understand or what seems contradictory to you.