Over HTTP you make one request, you get one resource back. Getting stuff to generate in multiple frames is not trivial.

A relatively sane approach might be to make your request to target="_top" and replace the frameset each time. Then store the results you want to display somewhere, and pass an identifier back to the browser in the src attribute of each frame from the generated frameset.

The browser will then request the two pages passing in the identifer, you can retrieve the actual page or the log based on the request. The data will then be displayed in the frame.

I can think of a couple of different approaches, for the non-javascript approach rather than trying to write to two frames at the same time, you can look at it from a different angle, have the log frame simply refresh periodically, and have the write_log method write the logs to a file.

sub makeframeset {
    # create document frameset. top area for ui
    # bottom area for XMLRPC trace
    my $self = self_url;
    print header,
        frameset({-border => "1", -rows => "1*,1*",  cols => "*"},
            frame({-name => 'main', -src => "$self?run=page"}),
            frame({-name => 'log', -src => "$self?run=log"})
        ),
    end_html;
}
sub write_log {
    open( OUT, ">>/tmp/logfile" );
    print OUT "$_<br>" for @_;
    close( OUT );
}

my $run = param("run");
if ($run eq 'log') {
    print header, '<meta http-equiv="refresh" content="10">';
    open( IN, "/tmp/logfile" );
    print <IN>;
    close(IN);
} elsif ($run eq 'page') {
        write_content('Main Area');
        write_content("<a href='self_url()'>Simulate Run</a>");
} else {
    write_content("running...");
    write_log("foo");
}
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The alternative would require a little javascript...

<script language="JavaScript"><!--
function write_log(msg) {
    parent.log.document.write(msg + '<br>');
}
//--></script>
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Then you could do something like this:

print "This is content area\n";
print "write_content('This is a log message');";
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Note that there are some other problems to overcome with the code you posted (for example, in the elsif($run eq 'page' ) section, you call write_content() twice, but write_content() provides headers and document wrappers, which means you will get two sets of content-type headers, two sets of document tags, etc).