I have a few different project with the same core.
All I need is to mark all not current projects as excluded to avoid searching through them (
To apply custom search use Scopes Settings/Preferences > Appearance & Behavior > Scopes to use it for Find in Path or Replace in Path.
I suggest to reorganize your folders, so that no unnecessary files are left in project directory. Also, you can specify Source Root by going to Settings > Project Settings > Directories and adding additional directories.