When using the possibility to create website from the front-end, the parameters are very limited. In this case, you have to prepare websites ready to use and that you will clone to build a new website.
Perhaps this is the solution.
See the tutorial video 13 that show this case.
www.jms2win.com/en/tutorial#jms12x-13
It is also possible to create specific "JMS Layout" to provide another front-end interface. So the look can be different.
When creating a website from the front-end, you don't need the "Joomla isntaller" as you are replicating an existing "ready to use" website.