color coding in cat6 networking

It's the same color coding as CAT5. Not that that really helps, but the link above should give you the correct colors.

In reference you your second (and more important) question. NO.
While it might work, it won't be compliant with proper CAT6 standards. Of course if you swap the Blue and Blue/White wires with the Green and Green/White, that won't necessarily be a problem, but there is a reason why pins 1 and 2 and pins 3 and 6 use the same color pairs. So while using Orange for pin 1 and Green for pin 2 might work, the electrical characteristics of the signals may slightly change and therefore would put you out of compliance with the proper standards.

In short, if you care enough to be using CAT6 instead of CAT5 or CAT5e for some reason, then at least be conscious enough to use the right colors.

You need to terminate cabling in either a 568-A or a 568-B pinout.

If you're looking down at an RJ-45 (8 pair, 8 conductor (8p8c)) so the tab is on the bottom and it's "pointed" away from you, pin 1 would be on your left and pin 8 on your right.

568B pinout:
1 - white with orange
2 - orange
3 -  white with green
4 - blue
5 - white with blue
6 - green
7 - white with brown
8 - brown

If you used a 568A pinout, you would swap the greens and oranges.

You CANNOT use any other color combination.  You have to stick to this combination to maintain the carefully electrically engineered characteristics and capabilities of the cable.  For instance, you can cannot wire them up "straight through" like a 110 punchdown color combination - blue, orange, green, brown.

You can use either the 568A or 568B - but make sure to use it everywhere.  If you switch them, A on one end, B on the other - this is in effect a crossover cable.

Hope this helps.

Ps. (you can wire it "straight" on patch panels in between if the panel says to.  If you're using an A panel, you can wire it B, as long as you know what you're doing and keep everything straight.  Document everything well.  Test to make sure you're doing it right - you don't want to get halfway through a panel and then realize you're doing it wrong ... (been there). :)

Out of curiosity have you done any network cabling before? Sounds like maybe not. Network connections are extremely fussy. Unlike telephone wiring where if you have continuity, it works, network cabling performance can be drastically reduced by close proximity to electrical interference, stretched or kinked cables, wire pairs being untwisted too far, jacket being removed too far, and poor connections at the end points. The problem is, chances are your network will work, but you cannot determine if due to some minor installation problems, packets are being lost and retransmitted such that the network is not working at full potential. I would not discourage you from wiring your own network, but it is extremely important when complete you have it tested and certified by a proper cable installation company using a Fluke  DSP/DXT, Wirescope, or equivalent tester. In some cities you can rent these meters. The tend to run >$6000 to buy.