According to most sources and users, iPhone 5S will not allow any sort of MobileSubstrate at the moment. This tutorial is done using an iPhone 5.
Using some jailbreak tweaks and apps, sometimes you are required to access these special settings through the iOS Settings "app". I mentioned earlier that this could not be achieved thanks to changes in iOS 7's design; however, this has been fixed thanks to a new tweak.
Add these repos to your sources in Cydia. To do this, visit the Cydia app and go to Manage.
Now, go to Sources.
In the top right hand corner, click Edit.
In the left corner, click Add.
Now, add these addresses exactly as they are written into the field again and again until they're all finished being added. Your phone may reboot after some of these and it may take a while downloading the necessary information, so please be patient.
Once this is done, download Mobile Terminal from Cydia. Also, download Bootstrap.
After those two have finished installing, open Mobile Terminal and type "su" without the quotations. The default password is "alpine" without quotations. If successful, there should be a # symbol which means you have been granted root access. Now type this without quotations "/bin/Bootstrap.sh". Your device will now reboot.
Once this is done, you should have all of your tweaks available in the Settings app. Below is a screenshot of what mine look like.
See where it says Adblocker, Browser Changer, and WinterBoard? This is what you are trying to accomplish. These are apps currently only available via Cydia and require access through Settings.
I can confirm that Browser Changer works. I was successfully able to open a link from Instagram into Google Chrome even though Apple set the default to Safari.
Any additional tweaks or apps that require Settings should now show up here.