Here's the thing... Package name and filesystem path have (almost¹) no intrinsic connection at all. The only reason they're normally the same is because of convention. But you should absolutely follow this convention because, even though Perl can handle it without problems, it easily becomes very, very confusing for humans trying to use the code, as your post here illustrates.

I suspect the reason you're not quite seeing the significance of the distinction is that, in this case, your package name and filesystem path are almost, but not quite, the same, so it's easy to gloss over that difference in your head. So let's rewrite things a bit to make it more obvious. In a file at My/Bar.pm, put

package Xyzzy;

sub say_it {
  print "It works!";
}
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Now, in your code, you load this file with use My::Bar; but there is no package named My::Bar, or even a package named Bar. The package is named Xyzzy, so you must call the sub with Xyzzy::say_it (or Xyzzy->say_it if you prefer, since it will just ignore all parameters passed anyhow).

If you move the module file to Some/Random/Place.pm, you will then load it with use Some::Random::Place;, but the package inside is still package Xyzzy, so you still have to call the code with Xyzzy::say_it, not Some::Random::Place::say_it. The path you use the module at and the package within the module are two separate things.

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¹ There is one exception. The one and only time that Perl cares whether the path and the package name match up is when you export symbols. This is because use Whatever; is equivalent to require Whatever; Whatever->import(); so, if the file Whatever.pm contains package Something::Else, and Something::Else exports symbols, that won't work because the use will implicitly call Whatever->import() (which doesn't exist) and not Something::Else->import().