Hi kcdesi,
We are really sorry for being late on this thread. Due to the upgrade of our support system, a number of forum questions were not pulled into our JIRA correctly and your thread question is one of them.
Anyways, I have looked through the give link above and saw that you are trying to install the JA Fubix template with the installed JA Nex template. That way will cause the problem with controlling and editting the JA Fubix template in backend.
The reason of problem comes from the big differences in template layout management and integrated features (responsive, Bootstrap, .Less) on the two system plugins (JAT3v2 for JA Nex and new T3v3 for JA Fubix).
The solution that we always suggest JA members in this case is keeping to use the default template with its system plugin (i.e JA Nex and JAT3v2) and disabling the rest ones. Or reversed.