only "do you understand?" you use do + base form of verb "are you understand?" is completely wrong. maybe "are you understanding?" but it still doesn't quite sound correct. "are you busy?" or "are you working?" make sense. so you see, are + adj/verb + ing.

Certain verbs are not normally used in the present continuous tense. These are: 1. verbs of thinking and opinion:agree, believe, expect, forget, imagine, understand....... 2. verbs of emotion and feeling: feel, hate, hope, need, like, love, want, wish....... 3. verbs of the senses: hear, look, notice, recognise, seem, smell, see*..... 4. verbs of having and being: be, belong, contain, have*, own... *The verbs "have", "see" and "think" can be used in the present continuous but the meaning is not the same as in the present simple. "Have" with an appropiate noun can mean :eat, drink, take, give: He's having lunch. "See" can mean "go out with or meet" : she's seeing a friend. "Think" can mean "consider": I'm thinking about the question. So, "understand" can be used only in the present simple tense: Do you understand?

Do you understand is a proper question. Are you is WRONG....either the person is intending to say "do you understand" or possible "Are you understanding...(this, that....)? Are you understanding what my reply is? hahha or Do you understand my reply? but never "Are you understand my reply?"

I believe all the answers above suffice your inquiry, only that the 2nd question: "Are you understand?" can be diverted to "Can you understand?". If you you are well versed in using the word "are", you can simply say "Are you able to understand" or "Are you getting what I'm saying?" Anyway, in terms of politeness, Both can either be polite or impolite depending on the tone of your voice or your attitude towards asking it, as "Do you understand?" is a blunt statement that implies one's behavior towards understanding a thing, while "Can you understand?" is rather asking someone if he's able to understand or having the capability of comprehending the meaning of. Moreover, you should also watch out the scenario and whom you might be talking to as they can be a slight annoyance and disturbing when asked wrongfully.