How to emphasize a word in writing?
Your example is just an example of possessive elision in Chinese. Both are acceptable and considered equivalent. None of the two has more emphasis than the other. 

One thing to note is there are two different types of emphasis, one being the emphasis of tone/mood, the other being the emphasis of meaning. In your case, it's the former. In English, the first type is often represented with italic and the latter with bold. 

There are many ways to bring the reader's attention to a particular phrase in a passage in Chinese. 

1) The official method, the underdot, as the name suggests, is placed under the characters that need to be emphasized. Sometimes a small circle is used as well:

  那只笔是他拿的.
         .


2) Another method is to use the squiggly underline (same as the one you see in MSWord when you have a spelling error)

3) Yet another method (but much rarer) is to use the normal underline, but this causes confusion in some cases, as it is also used to indicate proper nouns in Chinese in some older texts.

4) The first two methods are good for hand-written materials, but with the advent of typography, people are increasingly inclined towards using bold font to represent semantic emphasis and italic to represent tone/mood emphasis. This method is openly denounced by language purists due to the fact Chinese characters, unlike Western alphabets, look aesthetically displeasing when boldened or italized in a computer font. 

My suggestion for you is to express the emphasis in some other way. For example, you can spell things out: “她是我的太太, 不是你的!” Or if you are quoting someone, then: “她是我的太太.”, 他特别强调了‘我’这个字.