I need to add some mathematical procedure ( Algorithms) from already proved and published papers in my appendix. Is it fair and will it be considered in the similarity index/plagiarized work ?
Perhaps, you can just do the similarity check separately for the article and the appendix to have separate similarity indices. Anyway, 'copied text' indicated in the similarity or originality report doesn't mean that there is outright plagiarism; you just need to cite them properly.
Mathematical proofs are often included in the appendix to avoid cluttering the main paper. If you have cited the source clearly, it should not be a problem even if the plagiarism detection software identifies the algorithms as similar content. However, to be on the safe side, it would be a good idea to mention this in an email to the editor.
The Appendix is as much part of your paper as the body is. It must be fully referenced. Thus it is useful to include your References section after your Appendix.