Hi @jinxius Jeanette –
The CUNY Academic Commons was developed much before CBOX, and has a lot of customized code, and is not using the CBOX theme. So there is not a setting in CBOX that you are overlooking. I think you would probably need to create a child theme and make some template changes to achieve consistent footers on your blog sites.
In terms of the common header – I think that is just a BP admin bar, and shouldn’t be hard to mimic.
If you need more technical assistance about how, exactly, a consistent footer might be rendered for a multisite installation of a CBOX child theme – I can ask the dev team to point you in some directions.