The rule of the thumb is, use RTL paragraphs when writing Persian text (which might contain English text within it) and use LTR when writing English text (which might contain Persian text within it.)
There is an algorithm called Unicode BiDirectional Algorithm, the details of which is avaibale on Unicode.org. As you might have guessed, Word doesn't provide a correct implementation of this algorithm (nor do any other text editors that I know of to this date.) There's a library being developed called FriBidi, of which Behdad is the project maintainer, IIRC, which might help you, but not with Word probably. I guess Behdad would be able to make profound comments on this.
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