I usually manage FreeBSD over ssh from Windows or Linux PC.
Copy and paste works fine with ee(), when I use it remotely.
On windows I use Putty ssh-client, it supports copy some text by selecting it using mouse, and paste using right mouse button.
On Linux I use GUI terminal and ssh for remote access to the FreeBSD.
Linux GUI terminal supports copy and paste with Ctrl+Shift+C and Ctrl+Shift+V
In case of FreeBSD local console - I prefer to use mcedit. It is a builtin editor of Midnight Commander port.
It supports copy-paste via F3,F5 buttons and can insert text from a file and save selected text to a file.
So I had no troubles with copy-paste in ee() in case of remote usage over ssh.