We have been using gradle for about a year and have been somewhat successful with it. A number of features are still a little opaque, but we are getting there. I am not sure
I would simply put the following in TopProject/settings.gradle:
include 'Project1:SubProject1'
include 'Project1:SubProject2'
include 'Project2:SubProject1'
...
The only change required to the projects you currently have is to remove settings.gradle files from them as you can only have one setting.gradle file per project structure.