Just wondering if it's ok to have my shared-files in sub-directories in side the 'shared files' folder? or will only the files directly in that folder be shared?

usually it's ok as most clients scan the sub-folders also. on some you have the possibility to restrict the crawling of sub-folders. easist way to find out for your client might be to check the monitor (think each client has one) on which you can see what files you are sharing. otherwise
1) read the manual,
2) if this doesn't help: go the forum of your client and check if the question has been asked,
3) if not: ask there again.