run amuled on the server and connect remotely with webinterface or much better with amulegui under windows or linux. For windows there is also a precompiled version. very comfortable. The problem is, if you run amuled on linux on startup, then in executes as root. Though i access to downloaded stuff via samba, i alway have to change the permissions with ssh, because the downloaded files belong to root and choose another Incoming directory, because samba doesn't work with directories starting with dot i.e. .aMule/
hope, this could help