How to write a cover letter for a PhD position while involved in another PhD?
Just be forthcoming about the reasons why you're switching.  If you have evidence that you have a track record of success (grades, publications, etc.) in your former PhD program, there is little reason to believe that mentioning this information will count against you.  Even if you don't have a particularly "good" track record, it's important to be forthcoming about your experience nonetheless.

The key to a successful transfer into a different PhD program is how you justify changing programs.  This falls more into the category of your personal statement, rather than your CV.  If it is because you realized that you have stronger research interests in another field and wish to pursue research with a top professor in that field, then I don't think any institution would frown upon this regardless of your track record.

I'm not familiar with your track record, and I don't want to make any assumptions about you one way or another.  Thus, I want to address one more key issue:  If you are changing programs because to avoid "impending failure" at your previous PhD program, this will most likely be interpreted as "jumping ship" and institutions will not look highly upon this.  If you happen to be failing in your PhD program, you need to do some introspection and ask yourself some tough questions.  If a PhD is what I really want, why am I failing?  The more open and forthcoming you are about these questions in your personal statement, the more strongly you can justify your reasons for pursuing a PhD in another institution.