It may help if you said what software you are talking about. It also does not help talking about left and right panes since some software layouts can be customized. What is left to you is right or top for someone else. Bottom may be the transfer manager, it may not be.
When you transfer from the remote location to your local location are you logging in and then transferring files yourself, or are you allowing others direct ftp access to your account/server? When your software starts up is it set to automatically login to that remote site, or just start with the bare app?