The connection between azkaban and hadoop is weak.
You can, like you suggested, run hadoop jar. We tend to invoke hadoop through Java program or through the pig type. There are thoughts of increasing the hadoop interactivity by having better time completion percentage and to show job tracker usage as well.
For property propagation, a special property file is written by your jar that azkaban knows to pass to the next job. Unfortunately I'm not as familiar with this area as I should be. We'll need to update the docs for this behaviour.
Thanks,
-Richard