Doc Improvements

This adds a note about coordinate conventions in photutils (specifically, which axes of the data array the x and y coordinates refer to) as requested by @eteq.

Along the way, it also fixes some rst formatting (mainly single vs double backticks) and improves a section of the docs that were outdated.

Also also, fixes a bug where the `method` keyword was not being passed along by the wrapper functions (and so was being ignored).