Liz - when you design your chat(assuming a public chat) upload all the files to the same directory as you set it up for using the wizard - example: mysite.com/chat, you would upload all the files to public_html/what ever directory mysite.com is in on your server/chat.
To log in to the chat, go to mysite.com/chat
The option to log in with the software is for 1 on 1 customer service chat.
Currently, unless you're doing a customer service chat(1 on 1), there are no admin controls on the chat application.
Hope that helps clear things up some
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