How to determine similarity score of new manuscript against own yet-to-publish manuscripts? Considering the ethical and professional implications of self plagiarism, it is very useful to check new manuscript against old ones (which are under review and not yet published) to decrease self plagiarism. In a white paper by ithenticate (download from http://www.ithenticate.com/self-plagiarism-free-white-paper), one way to avoid self plagiarism is to significantly paraphrase those text which are need to be used in new article. However, I have difficulties in identifying the similarity percentage of my current work against yet-unpublished works. Online tools (that I know) check the manuscript against published works. I have 3 journal papers, 1 is published, 1 is under review, and 1 is under preparation. Now, I need to check the third one to see the similarity score. Any suggestion?
First suggestion: Never copy-paste material from earlier works, always write everything from scratch.

This prevents you from moving critical passages from one paper to the other. It is of course still possible to end up with a similar or even identical sentence by accident, particularly if you describe a method or something similar. If you end up using the same method for several papers it is also possible to simply reference your original description in subsequent papers. The Ithenticate white paper mentioned by you provides good advice. Yuo can slso visit the COPE (Committee On Publication Ethics) web site and search for self-plagiarism.

Second suggestion: Use the softwares such as iThenticate,  turnitin or the like depending what you are looking for. But, I would not blindly just look at percentages of overlap but focus on where the overlaps occur. If it is in the methods section describing a series of steps ina  process it is clearly not as critical as if it is in the discussion or conclusions. If you find overlap and you can identify what it is, then go to my first suggestion and critically review if you need to say it again.