Along with the new Pentium 66 machines was a new PCI ATA card. The new BIOS in the Pentium was richer so less work is needed to be able to use the new cards.
The biggest advantage of the PCI ATA card is the speed is dramatically better. The new PCI slot operates at 33 MHz which is a lot faster than the old 8-bit and 16-bit slots could handle.
With 3 or more PCI slots, Intel clearly wanted to make the new slot popular. The ISA slots are present for backwards compatibility. This makes the Pentium 90 an easier proposition for upgrades. The old 16-bit VGA card can be used until a new card can be purchased for the PCI slot.
Loading Windows 3.1 from one of the PCI cards was very fast. The difference from the ISA based 80386 and the new Pentium is astounding.
The new PCI ATA cards also are available with 2 headers to support as many as 4 hard disks. Most could only afford one hard disk and the few rich enough to have 2 disks means more bandwidth for each disk.
Older ATA disks immediately are faster suggesting the design of the old ISA was holding back the development of the onboard disk controller boards. New disks are fast with the PCI ATA card.
Intel is intending to ramp up the EIDE clock so that hard disk transfers can be faster. Hard disks are designed to deliver x number of blocks so the disk transfer area has to be big enough and the interrupt controller has to get the data off the buffer as it comes in. This is more or less the idea of why DMA controllers are present. The controller can handle the DMA and move data automatically without CPU intervention.