Subversion doesn't particularly care about your directory layout, there's no reason you have to change from what you have now.

To elaborate, it's typical to have separate projects at the top level of the repository each in a directory, and beneath this you have directories for different parts of your release cycle, for example /trunk, /branches, /tags. Beneath that, for example in /trunk, you have your project set up exactly the way it's always been set up.

So really this isn't a Perl question: How to set up your directories at the top level down to, for example, /trunk, is a subversion question and there are materials elsewhere that explain that. Beneath this, your directories are whatever you find useful for your project, and this is a Perl concern that has nothing to do with subversion.

If your Perl programs are interdependent in terms of their locations on disk, that complicates matters, but I'm not clear if that's part of your question or not, and anyway that would be a more general Perl question that's not specific to subversion.