Uploading files to 2 different domains

Regarding the topic's title above, I assume I need 2 different local browser files plus 2 remote files. Can someone help me to set up SmartFTP's local & remote folders to reflect this? Prior to now, I only used SmartFTP with a website I'd already set up, and all I had to do was to make small occasional updates, so this is a whole other ball game. Sure appreciate any help.