Once you have created the project via maven, you should then be able to import it in as a Maven project into IntelliJ, the following steps is how I did it the first time:
I first ran the mvn archetype generate for Thucydides + JBehave:
mvn archetype:generate -DarchetypeGroupId=net.thucydides -DarchetypeArtifactId=thucydides-jbehave-archetype -DgroupId=com.testing.app -DartifactId=SampleJBehaveProject
Then to Import the project into IntelliJ as a maven project.
1) File > Import Project
2) Select the location of the project. Click Next
3) Select "Import project from external model" and select Maven. Click Next
4) Check the Root Directory etc (defaults should be OK. Click Next.
5) If you've installed Maven 2.2.1, use Maven 2 profile, otherwise Maven 3. Once selected, click Next.
6) Click Next
7) On the SDK page, add one if none exists, otherwise click Next.
8) Use the default name (or change if you want). Click Next.
9) Click Finish.
CD into the project directory, then run "mvn clean install"
Once you have the "target" folder under your project you should then be able to do a "Run > Run AcceptanceTestSuite" in IntelliJ. To debug, then of course select "Run > Debug AcceptanceTestSuite".
Using these steps I have set up a few projects and have been able to successfully debug in IntelliJ.
Hope that helps.