I know how I can send files to a specific directory on a remote server using ssh, but I don't know how to specify it.
There are a few methods.
The simplest way if you're just transferring a file once in a while.
scp myfile.txt email@example.com:/home/user/
scp stands for secure copy and it transfers over SSH.
There is also
sftp firstname.lastname@example.org > cd /home/user/ > put myfile.txt
I guess the only real advantage to using this is that you can transfer multiple files without typing in your SSH password all the time. (If you don't use a keyring that is)
If you're going to be regularly transferring files take a look at
rsync. A simple usage of
rsync might look like:
rsync mydir/ email@example.com:/home/user/
But take a look at the man page as there are tons of options.
Finally, there is a
sshfs. With this method you can mount an SSH server to your local filesystem like any other filesystem, then you can just copy files into it.
sshfs firstname.lastname@example.org:/home/user/ /mnt/ssh/ cp myfile.txt /mnt/ssh/
Technically, the answer to your question is that you must specify where the file is. There is no magic.
For instance with SCP (which uses the SSH protocol) you would specify username@systemname:pathtofile
SCP then logs in to the system that you specify using the username and follows the path that you specify to find the file.