Add both databases to your solution. Set "build action" = content, set "copy to output directory" as "copy always".
Go into the Application Files dialog and see if it is deploying them as Data or just as Include. If marked as data, it will move them to the ApplicationDeployment.DataDirectory folder. If you don't want it to move them, change them to "include".
Also, here's a thread that has a post from mewith two links in it; ittalks about how to deploy a database with your ClickOnce application. You might want to copy it to a folder outside of the deployment folders in order to ensure it doesn't get overwritten if you open and close the database.
http://social.msdn.microsoft.com/Forums/en-US/winformssetup/thread/c8c55be6-be34-47cf-93fc-6cc0bf97f2cfRobinDotNet
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