Placement of Pinyin in relation to characters
As far as a "defined standard", I believe there are no official rules for pinyin placement. Texts in Mainland China are likely to place pinyin above the characters, while texts for foreigners differ in their approach. Sometimes even a single text will have different standards; for example, the New Practical Chinese Reader sometimes places pinyin above and other times places it below.

If I were to argue for one approach or the other, I would reason as follows: if the pinyin is to come in a block (e.g., a full paragraph instead of a word-to-word matching) then I would put the Chinese characters first and the pinyin second, to force foreign language learners' exposure to Hanzi without pinyin, and have them try to get through the characters as best as they can without resorting to pronunciation help. 

In the word-to-word matching that I think is your primary concern, I would argue for pinyin placed above the characters. The first reason is consistency with texts used by native speakers (though one might very well say consistency with native approaches is not in general best for foreign language learners). The second, more important reason is that the tone marks (more than most letters) may appear to foreign language learners as if they are part of the characters. Placing pinyin above characters allows the letters to serve as a sort of buffer between tone marks and Hanzi.

Nevertheless, I highly suspect that a longitudinal study on the difference between learning outcomes for foreign language learners whose texts had pinyin above and learners whose texts had pinyin below would show no statistical differences. If your intuition tells you otherwise, I encourage you to find a first-year Chinese teacher and see if you can institute such a study, as it would be very easy to carry out. More interesting, I think, would be to include an additional group for whom the text's lessons are first written solely in Chinese characters, with pinyin presented separately afterwards (as opposed to a word-to-word matching). I think it's possible that the latter approach would show small differences in learning outcomes between either of the former two groups (my guess is the block group would fare better; others might disagree) though I'm not convinced they'd be statistically significant either.