The resource exclusion/ resource filtering thing is fixed since m2e 1.0, so you shouldn't see the problem in JBT 3.3.
Depends how you imported the projects in your workspace. You need to import as maven projects.
You can try either right-clicking on your project > Maven > Update Project Configuration or going to the Project menu > Clean... That should force the maven-resource-plugin to execute;
As for installing JBT with m2e 1.2, you'll need to try the nightly builds of JBT 4.0 from http://download.jboss.org/jbosstools/builds/nightly/trunk/latest/all/repo/ or wait a couple weeks until we release JBT 4.0 Alpha1