Have two different applications using the same endeca engine. With just one LogServer you are not able to make a distinction between the log entries. To do that you need two different LogServers, each application writes to it's own LogServer. That part seems easy.
The problem is trying to create two different sets of reports. In AppConfig.xml it seems like I need to create duplicate entries for things like "DailyReports". And even that I think I can do. What I am not able to figure out is how the DailyReports gets kicked off. How it is started. In the Workbench all you have are two check boxes, one for daily and the other for weekly. What do those hook up to, to kick off things off?
As Pravin mentions, the checking of those boxes in Workbench triggers scheduled jobs within the EAC that kicks off the scripts at the appropriate time/day. But as you've noticed, there's not a ton of flexibility and you don't get cron or Windows Scheduler-type capabilities.
If you need to do something special, you can manually kick off the report generation scripts from your control directory using the runcommand.bat (or sh) script or place the command into a cron/Windows Scheduler job:
For example, to kick off the WeeklyReports job, you would do this:
runcommand.sh WeeklyReports run
So, assuming you go down the route of creating multiple ReportGenerators and scripts, you would create a job to kick off the new script you've created at the appropriate time.