In cgi, a message to STDERR will generally show up in the httpd's error log. For non-fatal errors, Perl's warn will do the job. For fatal ones, die.

You can keep error messages in a variable by opening STDERR to a reference to that variable. Something like:

{
    my $errors;
    open local(*STDERR), '>>', \$errors or die $!;
    # do stuff, can call external functions that warn or die
    if ($errors) {
        print error_template($errors); # however you do that
        exit 0; # or non-zero if we want to tell the server we failed
    }
    # maybe do more stuff - success branch
}
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