The firewire or USB "bus" is comprised of the internal interface (the communications chips forming the firewire and USB controllers), the physical connectors and the cable going to the external device (disk drive). For the best data handling capacity (throughput) it's best to not use an external USB hub if you can avoid it. USB hubs have switching and other active circuitry and need a power source which just complicates things. If the external drive is the only thing on the "bus", there is no need for a hub. The Macbook Pro has (2) USB ports and (1) FW 800 port. Those go directly to the external USB drive, and the audio interface through short cables (1 meter and 2 meters, respectively).
In Logic Pro, when a project is started you simply set the directory path to the storage device. Logic creates a "take" folder on the drive and places all tracks there as well as all edit and processing directions. I have templates set up for all of the possible tracking configurations I use with various interfaces and built-in or external mic pre configurations for between 2 and 16 tracks. The templates live on the system drive, but once a new project is started, the directory path points to an external drive and everything is stored there.
I usually set up a master project folder on the external drive [manually] before starting a new project, and then everything goes into it. That makes it very easy to quickly and fully back up a project by simply copying the one master folder. That fits my work-flow because my projects are all independent and don't share any content. I strictly do recordings of acoustic instrument performances, and don't use virtual instruments so I have very simple configurations.
The Apogee Ensemble interface is automatically recognized when it's turned on. It does come with a (more detailed) configuration and control program "Apogee Maestro", but it also is recognized directly from within Logic Pro via a menu accessible control panel. Access to the interface is completely automatic and transparent as long as the computer is booted up before the interface is turned on. The Ensemble I/O is highly integrated with Logic Pro.
Other interfaces are accessed through the Mac Audio/MIDI control panel.
For someone who is composing within Logic, and who may use specific instrument tracks in multiple projects, a different system of file organization probably would be better and would avoid unnecessary duplications. Logic allows a lot of flexibility of where and how files are organized.