I use rsync for that sort of thing. This is a linux tool so you'll need to install cygwin [cygwin.com] to run it on Windows though. Wait, is your hosting account Windows or Linux?

hosting account is linux

If you have shell access to your Linux account, zip or tar/gzip your files and uncompress then on the server. If you have to do this repetitively, you can set up a cron job to run a script that uncompress the uploaded file for you.

OK, if it is linux just check that rsync is installed on the remote machine.
ssh in and then do

which rsync

Then, from your local machine (after you've installed cygwin) do

cd /cydrive/c/path/to/your/dirthathasthestuffyouwanttoupload

rsync -ave ssh * user@your.server.com:./pathrelativetoyourhomedir/

If it gets interrupted just run this again. Rsync will only try to upload files that were not uploaded previously.

If you use linux on your home machine, and only have FTP access to the server, then use ncftpput from the command line.