This is the three parts that I'm using on my Jekyll blog (http://voxpelli.com/) to add Flattr.
I add the "default.html" part in the bottom of the default layouts HTML (the one used by posts). I add it just prior to closing body-tag. Make sure to change the "uid" parameter in the s.src variable to be your Flattr username.
I then add the a-tag in "post.html" in the place where I want the flattr button to appear. Since my blog supports both swedish and english posts I define a language attribute - if you don't use that in your Jekyll-blog then feel free to leave it out. Just be sure to change the domain in the href-attribute to be to your site.
Lastly I add the "default_head.html" part in the head-section of the default layouts HTML (the one used by posts). I also define a language attribute here - if you don't use such an attribute in your Jekyll-blog then switch it to something else or leave it out. Make sure to change the domain and to change the "uid" parameter in the s.src variable to be