Many memers already gave good explanation, so my message might overlap with many of them, but anyway...
First of all, Japanese grammar can be very much difrerent from English and other European languages.
1. Function of the word (subject, object, verb, etc.) are not decided by its location in a sentence. In English the word order is basically strict, so there's a definite pattern such as S+V+O or S+V+C.
In Japanese language word order is loose comared with English.
Topic(not necessarily the subject of verb)+[ ]+predicate.
2. There's no "preposition" in Japanese. Instead there are many "particles" which is placed "after" the word to modify its preceding word.
some examples of particle
ga : to indicate its preceding word is the subject of a verb
wa : to indicate it is the topic of the sentence (i.e. what the speaker is talking about)
ni : to indicate the place or direction
wo : to indicate its preceding word is the object
- The cat caught the mouse.
- The mouse caught the cat.
In English, the word before the verb means is the subject of the verb, so the above two sentences mean different things.
- Neko ga nezumi wo tsukamaeta.
- Nezumi wo neko ga tsukamaeta.
neko : cat
ga : particle to indicate the subject
nezumi : mouse
wo : particle to indicate the object
tsukamaeta: past form of tsukamaeru = to catch
In Japanese, both of the sentences mean the same thing - the cat caught the mouse, though in the latter more emphasis is placed on the mouse which is placed at the beginning of the sentence.
You can see that the location of each word does not affect the function of the word in a sentence.
I think that "kore wa nihongo de nan desu ka" is OK for "what is it in Japanese?".
"Kore wa nihongo de nan to iimasu ka" (what do you call it in Japanese) might sound a little more polite.
I think that if you are really new to learning Japanese, you are on the right track - first learn basic expressions with English translation, and after a while, when you learned some grammars, how verb/adjective conjugate and how each particle works, then you'll start to see the sentence structure.
Just my two cents worth.