As of late my relations with my mother are getting worse and worse. I think she still loves me and she probably wants to help me, but the way she does it... let's say that she does more wrong than good. I'm studying and right now I'm in home for summer holidays. I should already finish my studies, but because of few failed coursed i will be going for another year. Mother probably tries to motivate me to get fit etc. but the way she does it? Is probably one of the most demotivating thinks for me I can imagine. She tells me I look like a "monster" (I have 80 kg 175 cm height male) I'm ugly and and similar. When she tells me something like that, I'm stoping to care about my looks, because such a blatant lie sound stupid. I know i'm not fit, but a monster?

Well, to tell you the truth I don't care she can say whatever she wants, but lately something much worse happen.
I'm living in Poland, and we have World youth days right now (The Pope came and he speaks with young people from the entire world) Whenever this topic is shown in the News, she always says to me that I should look how youth have fun there, for what I respond "Yeah that's nice, I don't really care" She then always goes ballistic on me (I'm atheist) to the point when she says things like "Atheists don't have brain" to even something like: "You should go to Syria and kill people like that criminals, because that's what people that where believers and stopped to are doing".

I understand that she would like me to be believer, but I'm not. Is there a way to rationally speak with her and make her understand that? I don't think she is mentally ill, but maybe I'm doing something wrong?

In my experience, people of very deep faith that are not all too educated about not just their religion but other ones as well, can't really understand the thought process of atheists/agnostics/etc, so I don't think you can rationally get to her on that matter.

As far the "motivation" part goes, I assume you have explicitly told her that she isn't helping? If not, maybe you should, although depending on your mother it can easily turn into a fight (she'll call you ungrateful and stuff). Other than that, the only way to solve the entire situation is to make her understand that she can be making things wrong, and to do that you might have to get in a pretty big fight with her.

Hope I might have given you some new ideas and do let us know what happens.