Juju/Puppet service's configuration files
Juju has been primarily targeted towards ec2/rackspace and other cloud based deployments. You can probably use it in a traditional data center deployment as well.
If you intend to use Juju in a traditional datacenter or Colo environment, then you may find that Juju and puppet do mostly the same thing. Meaning, you are better off using one or the other, not both.
As for your 2 questions:
- I am not sure what specific bits you intend to package as rpms/debs. You can use puppet to install custom packages that you create, if thats what you mean.
- In the puppet world, one way to deal with differing configuration files, is to use puppet templates. Templates and puppet manifest code can get their information from backend data sources, using the ENC features, or add-ons like Hiera.
If you want to deploy your service on ec2 or other services, both puppet and juju will work fine.