David, if you are using DT Pro Office and select one or more messages in Mail, then choose Message > Add to DEVONthink Pro Office, the message(s) will be sent to the group designated in Preferences to receive new content. That works on my computer.
But if you chose in Mail the Mailbox > Add to DEVONthink Pro Office command, the selected mailbox(es) would be copied into an Archive group at the top level in your database.
If you are using DT Pro instead of DT Pro Office the mechanism for capturing a copy of an email is different. At the moment, I don’t remember whether it is sent to the top-level or to a set destination.
One of your comments interested me. You noted having to close your groups in order to get access to the top level. That’s not necessary, as you can have multiple view windows open, as I always do.
In Preferences > General - Interface check the option to always open groups in a new window. Now, if you double-click on a group it will open in a new window. That’s especially useful if you are working on a project group that contains subgroups.
To open a new top-level view, choose File > New Window.
Some scripts do send new content to the top-level view, regardless of Preference settings. Just switch between open views using Exposé – that can be done by swooping the cursor to the top right screen, or by choosing F10 (on a laptop, fn + F10), then click on the image of the desired view. Those are default settings for Exposé in System Preferences, but you can modify them if you like. I find Exposé to be a neat element of OS X. Right now, I’ve got 13 view and document windows open in my database and it only takes a moment to bring the desired on forward.
Note that the Groups panel (Tools > Groups) is convenient for dragging an item to a new group location, even if you are working in a partial view of the database. And because the Groups panel can float above all applications it’s also convenient to drag one or more files and/or folders from the Finder to any desired location in a database.
