I'm sorry I can't give you a real detailed explanation, but the PCI latency controls how the various PCI interfaced components intreact and get access to the CPU and memory. Optimizing it improves data transfer speed. This is most noticeable in IDE drive access.
What you will find available is an official VIA patch and the George Breese patch. Which one will do you the most good may depend on which BIOS and motherboard you are running. With my A7V333, BIOS 1008 the VIA patch made only minor improvements. The Breese made a huge increase in my RAID speed and some increase in the regular IDE speed.
Download and install it. I've never heard of any negative effects.