I found this a real problem when I began. You get used to it but it does take some practice. I find it better to understand what is actually being said, and to start to think that way. In the example you gave leche con chocolate is really milk with chocolate. Which it is, it's just more descriptive than chocolate milk. I have found that much of the order is a way of avoiding possessives for nouns. For instance, la mujer de mi hermano, my brother's wife, is in the order of "the wife of my brother" in Spanish. It's the reason I find it necessary to think in another language rather than just translating & saying the words. Hope that makes some sense.

You're probably thinking of the placement of adjectives. In English you usually put the adjective before the noun, as in, the white house, but in spanish, it goes after: La casa blanca. Thus, using your example, chocolate milk, would be, leche chocolate, but like most languages, in spanish we either say, Leche con chocolate (milk with chocolate) or I have also heard some say, leche de chocolate (milk of chocolate). I think kids would say the latter. So is a matter of learning the rules and then practicing. I think in other languages the the verb comes after the pronoun, so imagine talking like this in English---Today late was i because came the bust late. I believe German and dutch have that construction, so from that perspective, spanish is not so bad.