Since I can't easily tell the two apart from the command prompt, I don't really how to be sure if anything I put in has worked.
Tell apart STDOUT
? Just redirect them to separate files:
perl yourscript.pl >stdout.txt 2>stderr.txt
Although I feel local'izing the file handles is cleaner, as suggested by JavaFan, you could alternatively store them. Then re-store them. That way, you'd have STDERR available in the block if you needed it.
my ($out, $err) = (*STDOUT, *STDERR);
*STDERR = *STDOUT;
# pod2html code here
*STDOUT = $out; *STDERR = $err;