In inline mode, traffic passes into one of the appliance's Ethernet ports and out of the other. When two sites with inline appliances communicate, every TCP connection passing between them is accelerated. All other traffic is passed through transparently, as if the appliance were not there.
Configuration is minimized with inline mode, because your WAN router need not be aware of the appliance's existence.
Depending on your configuration, inline mode's link-down propagation can affect management access to the appliance if a link goes down.
Inline mode is most effective when applied to all traffic flowing into and out of a site, but it can be used for only some of the site's traffic.