Yes, you will need to put Baubles into the 'mods' folder, just like in regular environment.
To add a library from repository, you will need to specify the repository url and a dependency. Example for Just Enough Items:
repositories{
//the repository that contains the libraries
maven{
url "http://dvs1.progwml6.com/files/maven"
}
}
dependencies{
//the dependency
compile 'mezz.jei:jei_1.10.2:3.14.5.406:api'
}