So, you're looking to publish the "instances" that the client application generates, is that correct?
Unless the instances themselves are created in BOE (i.e., run from a report template that's already been published in BOE) the reports will NOT show up as part of the standard BOE structure - that is, navigate to folder, click on Report Title to view latest instance or click on History and then on the instance that you want to see.
Having said that, there are a couple of ways that you can do this. For both methods, I would set up a folder for each report that has the report title. I would then publish the file with the Title set to the report name plus the date it was run.
1. Publish the report with data. The trick to doing this is that BOE still has to be able to log in to the database that the report was run on. It doesn't refresh the data, but for some reason it still has to be able to log on. (I know this one from experience!) The report will then be viewed through whichever Crystal viewer the users have set up in their Preferences.
2. Export the report to PDF or Excel and publish that file. BOE will then know how to display the file. This code is easier than for step 1, but the users won't be able to export the report to a different format.
I have example code for both methods. Let me know which one you're interested in and I'll post it.
-Dell