Yes, I'd put the HD first if it is a FW800 drive. IIRC, the Mac will communicate at the speed of the slowest link between it and a given device, so it will talk to the HD at S800 speeds, but will talk to the interface at S400. By putting the HD first, the bandwidth available to your hard drive can easily quintuple.
A simple example: if your audio interface uses 100Mbps worth of isoch bandwidth, on a FireWire 400 bus (half duplex), you would have 300Mbps total for disk I/O. If half of the isoch bandwidth is going to the device and half is coming from the device (for example), then on a FireWire 800 bus (full duplex) it would be taking 50 Mbps each way, leaving 750Mbps of incoming bandwidth and 750 Mbps of outgoing bandwidth, for a grand total of 1500 Mbps left over for disk I/O. Much better than 300.