The ACCDB file should be in the same folder as all your other source files, i.e. VB code files and the like, because it is a source file. When you build, which is done each time you debug and when you publish, the code files are compiled and the output, i.e. the EXE is written to the output folder and any other files that are required are copied there too, e.g. the config file and the ACCDB data file.
When you publish, the contents of the output folder is packaged into an installer. It should be a Release build, rather than a Debug build, that is deployed. I don't use ClickOnce so I'm not sure whether that happens automatically or you have to change the build configuration. I think it's automatic.
Have you looked that Publish properties to see whether the data file is being included?