Yes they are the same phrase technically however I will say in English it sounds more natural to say the first one which is "Do you want me to pick up some books for you?"

"Do you want me to pick up some books for you" is correct standard English. "Do you want me to pick you up some books" is not correct standard English, although it is normal in some non-standard varieties of English that consider it to have the same meaning as the first sentence. The reason for the difference is that in both sentences the word "you" is the indirect object, while "some books" is the direct object. Verbs in English may be either intransitive (they do NOT have a direct object) or transitive (they either allow using a direct object or they require using a direct object). Phrasal verbs may also be either intransitive or transitive. Some transitive phrasal verbs are inseparable: they do not allow placing other words between the main verb and the phrasal particle. For example, "I ran into a car yesterday" (I accidentally hit a car yesterday) is correct, but "I ran a car into yesterday" is wrong. Some transitive phrasal verbs are separable: they allow placing some direct objects between the main verb and the phrasal particle. For example: "I checked out the book (from the library) yesterday" is correct, and "I checked the book out (from the library) yesterday" is also correct. However, if the direct object is a pronoun, it MUST be placed between the main verb and the phrasal particle if the phrasal verb is separable, and if the direct object is longer than a few words it MUST be placed after the phrasal particle. For example: "I checked it out yesterday" is correct, but "I checked out it yesterday" is incorrect. In standard English it is incorrect to place an indirect object between the main verb and a phrasal particle; only the direct object may be placed there. For example: "I checked out the book for you (from the library) yesterday" is correct, and "I checked the book out for you (from the library) yesterday" is also correct, but "I checked you out the book (from the library) yesterday" is wrong.

"Do you want me to pick up some books for you?" Yes, although it sounds odd because normally someone would want to pick out the books for himself or herself. It would sound more natural if you were asking about something like groceries -- some apples, some oranges, some milk.