ATA cables are unterminated (unlike SCSI, where the ends have a terminating load).
The standard for Ultra-ata (80 wire) cables, is that the Blue (Host end) MUST go to motherboard or controller (or the cable will not work as 80 wire at all).
Where there is only one drive, it should be Master (solo slave is an invalid configuration), and to minimise signal reflection, it should be at the end (black connector), even though it does not have a terminator as such.
The Slave than goes on the middle (brown) connector.
If you have Master/Slave rigged the opposite way, it's probably ok, but it's definitely nonstandard.
Using the end first, rather than using a shorter span, is correct for 40 wire cables, other than for 40 wire with cable select, which places the Master (or only) drive on the middle connector, leaving a tail.
It is also generally ok to use an 80 wire for non-Ultra drives (ATA/33 or less), but not to use an 80 wire cable on a non-ultra controller, since it may not ground the extra screening wires correctly.
The 80 wire cable does one thing only - supports transfer rates above 33Mb/s.
16x DVD peaks at 22Mb/s, so ATA/33 mode is not a problem if only one drive is active on the cable.
Several DVD-ROM drives support UDMA-3 (44Mb/s) on 80 wire cable, and a few DVD-RW drives support UDMA-4 (66Mb/s).
Current hard drives are normally ATA-66/100/133 - and the BIOS normally warns you at boot if you are losing potential throughput by not using an 80 wire cable where it's needed for maximum performance.