How to configure a Gradle command-line switch

I have a multi-project Gradle build with about 200 sub-projects. When I open the build.gradlefile in IntelliJ, an IntelliJ project with all these sub-projects as modules is created. I have two problems with this:

1. I only work on a small subset of this project, so I prefer to have only those open in IntelliJ
2. IntelliJ collates dependencies from all sub-projects into a single flat list and uses that in the CLASSPATH whenever I run any class from within the IDE.

For legacy reasons, I cannot break the project into disjoint subsets. So I created a my.settings.gradle file with only the parts of the project I care about (and ignored this from version control, so the rest of the team will not get it). This works great on the command-line when I invoke gradle with the --settings-file my.settings.gradle flag. I have couple of questions:

1. How do I force Gradle to pick up my custom my.settings.gradle file when I run gradle from within my project tree?
2. How do I make IntelliJ pick the my.settings.gradle file?

I am using IntelliJ IDEA 13.1.3 and Gradle 2.1.

(cross-posted at StackOverflow)