See the system command, or perlop's discussion of backticks. Either will allow you to execute a batch file.

As for whether it's better to compose a batch file, or handle all the work directly within perl, I would probably opt for the latter most of the time. However, without knowing more about your problem it's impossible to say definitively which approach is better. I generally find it less complex to just do the work in one scripting language instead of two. But that doesn't mean there are no cases where invoking a batch file is a good way to do it.

In particular, if the objective is just to get the job done, and you already happen to have a couple batch files written that are doing the job for you, there's nothing wrong with simply using perl as the glue to bind them together. If function is more important than fashion, use the tools you already have at your fingertips, and glue them together with Perl.