So this is what I did:

if ($up_dir_local && $up_dir_remote) {
print "Preparing to upload folder $up_dir_local to $up_dir_remote \n";
sleep 3;
if ($sftp->mkpath($up_dir_remote)){
if ($sftp->rput($up_dir_local, $up_dir_remote)){
print "The directory \"$up_dir_local\" was uploaded to \"$up_dir_remot
+e\"";
} else {
print "\"$up_dir_local\" or \"$up_dir_remote\" could not be found. Che
+ck your path!";
}
}
}
[download]

And this works for copying folders where the mkpath command creates a folder before the rput command copies it. But this does not work for copying files because the mkpath command creates a folder with the files name where it places the file. My question now is how would I modify the mkpath command to ignore everything after the last '/' so that it doesn't create a folder with the files name.