I think 45 mins in Atlanta is enough time; others may disagree. We're going to be making a 39 minute connection in Detroit next month.
As for the first ferry, I can honestly say I really don't pay any attention as to what ferry to take. I book Kevin as our taxi driver and ask him to take us to the next available ferry. Works perfectly. If you have to wait, get your C&I forms and go upstairs to the Pump Room. Fill out your forms, have a drink and adjust to island time. :-)