You're conflating two different issues - the category rating (Cat5e vs Cat6) refers to physical properties of the cable itself, specifically the bandwidth (in MHz) that can be successfully transmitted within a given noise/interference window. The physical implementations of various Ethernet specs take this into account (thus 1000BaseT vs 10000BaseT, etc).
The order of the colors is a wiring specification. There are two common versions in use: EIA-TIA 568A and EIA-TIA 568B. In general you want to make sure that both sides of a given patch cable are using one or the other. If you make a cable with one side A and the other B you'll have a crossover cable (not generally necessary with modern auto MDI ports and NIC's). The same logic applies to jacks as well, of course, and best practice within a given cabling plant is to choose one spec and to stick to it.
Also keep in mind that the order here is more than just cosmetic - keeping transmit on its twisted pair (..and separate from the dedicated twisted pair for RX) is crucial to noise rejection techniques, etc. 568A and 568B are both equally performant, but splitting pairs is most definitely not!