How can I do my own batch conversions? ...but update Kaltura as if it did it?

I am new to Kaltura. I am working with Version 3.0.0, and have just begun to get going. Sorry if this is already covered somewhere else, but I think it may be a unique thing I am trying to do.

Normal scenario: A user logs into my PHP site, and uses the page I have to allow them to upload a new video, or uses the batch upload screen in KMC. The single file upload uses the Kaltura API to upload the video.
Once the user does this, the normal batch processing would kick off conversions for each of the flavors in that customer's Profile.

Here is what I want to do:
Instead of normal batch processing of all the flavors (each in their own batch job), I would just like to have my program (or I could do a Java process or whatever) , called once after the content is uploaded, and instead of all the individual flavor jobs, to have my program figure out how to do all the conversions according to my special needs, and THEN, put everything into Kaltura so it thinks its normal batch processing has done each of the conversions (I guess including the "SOURCE" one).

So, only one use of my special program would get called once (for a single uploaded movie, or multiple times in the case of a batch upload of files), and then ALL the user's profile flavors would get created by my special program, placing the converted media where Kaltura would have, and then the user could see them in their content in the KMC.

I don't necessarily have to make use of the KMC to see status of individual flavor conversions (in fact I will have my own version of that), but in then end, I need Kaltura database tables to be updated properly so everything else works.

Hope that makes sense,
Thanks for all the help,
Karl