Hello,
JoomSEF will only process the metadata you enter for the content (articles) or that you enter in URL editor viewer.
You should be able to test this simply on any article.
If you do not see the metadata, then something is not working properly or there is some conflicting component.
As regards cooperation with 3rd party metadata generator I cannot guarantee that. That would depend on the way, how such generator is written and how it is submitting the metadata to Joomla to display.
If it is written according to Joomla coding standards, then I am conviced it should work right. (the problem is, there is not much such components available, especially not for free)