Web Site Uploads

Is there any way to upload a complete site in one go and then synchronise thereafter ??

I have tried drag and drop of all items but the results are -

i) The contents of subdirectories do no get uploaded unless I drag and drop them individually
ii) I have to go throught the "Replace" or "Skip" thing for every file.

This is a very tedious exercise for a large website, especially when developing.

Any ideas or advice ??