For a quick guide on configuring these plugins and using them together, check out the Getting Started with the Jenkins Plugin page.
You can invoke Jenkins from FlexDeploy using shell plugin(s), see Invoking Jenkins job from command line for quick reference.
If you are looking to migrate Jenkins jobs to FlexDeploy, see Migrate Jenkins job to FlexDeploy.
The FlexDeploy Plugin
The FlexDeploy Jenkins Plugin offers the ability to get an from a completed Jenkins build and put it into the FlexDeploy artifact repository. Once the artifact is brought into FlexDeploy, we can use it in any project build or deployment.