Ok, seems like it is picking the first wb-resource path in the .settings/org.eclipse.wst.common.component file..
<project-modules id="moduleCoreId" project-version="1.5.0">
<wb-module deploy-name="hcbb">
<wb-resource deploy-path="/" source-path="/src/main/webapp"/>
<wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
<property name="context-root" value="hcbb"/>
<property name="java-output-path" value="/hcbb/target/classes"/>
</wb-module>
</project-modules>
Just changing the ordering of these makes it work as expected for the most part. It's still complaining about missing attributes on my component. Need to look more into that.