Hi @jennychika
Unfortunately, there are no strains already uploaded as references in StrainPhlAn, any strain you want to add as reference genome in the tree should be manually added with the -r parameter. Please, have a look at this post: Identifying Strain Names
For your last question, no, MetaPhlAn should be run on the reads (or on the a sam/bowtie2out file produced already by MetaPhlAn) and StrainPhlAn should always start from the sam files from MetaPhlAn.