Is there a way to have the scheduled searches run in the background?
I have a daily search set up for a writing project, and it’s something I really, really, really do not want to pop up when somebody is looking over my shoulder.
What schedule options do you have set?
It’s set to search new sites every day and ignore the cache.
There is no explicitly “silent” mode, but if you can minimize interruptions if you turn off all of the “Interface” settings in the “Actions” tab, and then in “Schedule” set the search to run at a time of day when you’re less likely to be disturbed and select the options “Quit when done” and “Close window”.
In the actions tab, there’s not one option that’s marked. Not even “zoom and bring to the foreground” (however that’s called in English), but it big fat does it anyway.
Where do the results go, if I select “quit when done”?
The list of new results of a scheduled search will be emailed to you (if you set up that option), and the search results will be saved to the Archive.
More generally to what Bill posted, results are handled in whatever way(s) are configured in the “Results” section of the “Action” tab, and then DA quits.
Thanks guys, I had tomatoes on my eyes once again 
Is there a way to send it to a specific folder inside DEVONthink?
Now that I think of it, is there a way to limit the number of results? I know there’s a way to limit the results per module, but not overall.
The results will be sent to DEVONthink in accordance with the destination specified in DEVONthink Preferences > Import - Destination. As you wish the scheduled search to be “silent” I assume you want the files to be sent to DEVONthink without your intervention. In that case, you would probably want to set destination as the Global Inbox.
The only option affecting number of results is the number per plugin. (And, of course, the number of “new” pages found on successive searches.)
After Hurricanes Katrina and Rita I put together a DEVONthink Pro database that was useful to health care professionals for evaluation of impacts on Louisiana’s health care infrastructure (it was devastating in some areas). I used DEVONagent to send some 10,000 search results to DEVONthink, then used DEVONthink searches to help organize and winnow down the database to about 5,000 documents. Took 3 days of long hours to produce the database.
Another possibility is to use a secondary user account to perform silent background searching. The results could be emailed or added to a local copy of DEVONthink and synchronized with DEVONthink on the primary user account. Okay… that’s probably overkill 