First; I suggest you use the latest ubiboot, the vestion 0.3.6 is fairly dated, released on January 2014...
The latest is 0.3.9 which you can find from http://swagman.org/juice/ubiboot/ubiboot-02/
Seel also the changelog on https://github.com/juiceme/ubiboot-a.../doc/Changelog

As for configuration; you need to know and specify the location of your OS partitions and kernels; ubiboot does come with sane defaults but even that of course requires that you set up your device as in the instructions.