"The SCImago Journal & Country Rank is a portal that includes the journals and country scientific indicators developed from the information contained in the Scopus database (Elsevier B.V.)." http://www.scimagojr.com/aboutus.php
So it is simply based on papers published through the Elsevier group. For their fields, see http://journalfinder.elsevier.com/
Science Citation Index is a rival index, published by the Thomson Reuters group of publishers. http://ip-science.thomsonreuters.com/cgi-bin/jrnlst/jloptions.cgi?PC=K
So, it is simply based on papers published through the Thomson group.
My understandings are then:
1. If, for example, you publish your paper in an Elsevier journal, and you are cited by an author publishing in an Elsevier journal, you will get credit in Elsevier, but NOT in Thomson.
2. If, for example, you publish your paper in an Elsevier journal, and you are cited by an author publishing in a Thomson journal, you will get credit: neither in Thomson nor in Elsevier!
The purpose of these indexes would then seem to be to enforce loyalty to the publishing group. This is unfortunate as it would enforce publication only in the group.
If your fields publish, for example, mainly in Elsevier and not in Thomson, this may not be problematic. However, today research is multidiscipinary, and this creates problems. By being calculated on differing publishing bases, there is no way that figures in these two indexes can be compared.
Google Scholar and ResearchGate each have their own indexes, but these are more publisher agnostic, and therefore more balanced. However, even Scholar and ResearchGate have not been given permission to access all papers.
My advice to you is to target a good journal covering your fields, and not to worry about indexes.