Well, you can step through eval'd code, but you probably won't see the source lines since the debugger gets access to the source lines by reading from the file that Perl read from before.

Breaking on Module::function should work provided that the module has already been required. Of course, there are lots of fun things that modules can do that make this break. Autoloading is the most common. For example, much of CGI is generated when you need it, which makes debugging that code nearly impossible (because the code for most of the subroutines was eval'd).