.htaccess for Subdomain and Subfolder w/SSL

Typically if your subdomain’s root is the folder with WP installed, then just create a .htaccess file there. That always works for me.
Example:

public_html -> 
   random
   etc..
   mywpfolder (the wp folder)
      wp-admin
      wp-content
      etc..
      .htaccess (create htaccess file here or simply copy/paste the primary one here)

EDIT

Do you have the other installs in your domain root or the subfolder root? In any case adding the htaccess file to the folder that has your wp-admin, wp-content, etc should work for that WordPress install – it shouldn’t affect other installs. Unless I misunderstood your question.