I happen to build and troubleshoot computers for a living. So that has to stand for something. 
You should have no problems with the onboard stuff. As posted before, you can simply disable it in the BIOS, after a little hunting for the options. The problems that you speak of were valid, say, four or five years ago. But anymore, I actually recommend the onboard stuff because it cuts down on compatibility issues.
If you need an example, try to figure out the new AGP 2X/4X/8X “standard” in video cards. Basically, 2X is compatible with 4X. 4X is compatible with 8X. But 2X isn’t compatible with 8X. And that is only if the motherboard accepts the new card. It’s starting to get out of control (again).
A network card is a network card is a network card. They all act the same way. Very little difference in performance.
I’ve found, unscientifically and unofficially, that onboard sound is equal to or better.
The only reason you would want a second LAN card at this point is if you wanted to do a thing called Multihoming to your computer, for the sake of Multiplexing. That is, you devote one card for incoming data, and the other card for outgoing data, essentially. Mathematically, this exponentially increases your bandwidth. The downside? Few, if any, ISPs offer this service. You need to buy another user account and IP address for the second card, and there is usually a service charge tacked on top of that. It is quite expensive.
But let’s get more practical.
Since you mentioned you would be getting multiple computers in the future, think of the logistics ahead of time. Two computers is easy - just run Crossover Cat 5 (very important, or it won’t work) between the two LAN (aka Network) cards.
But three computers is different. You can simply buy a hub, router, or switch (I have to recommend the switch) and plug all three computers into the device, so they can communicate with each other. Or you can hook the two computers on the ends into each of the two LAN cards in the computer in the middle. In this last example, the middle computer essentially becomes a low level server for the two computers on each end. After some configuration trickery, viola, you have a peer-to-peer network. LAN party away.
By the way, if you go shopping for a hub/router/switch and LAN cards, look for the package deals. Those are of the best value, plus the compatibility is pretty much guaranteed.
About the other Asus motherboard, with the RAID and Firewire. The difference in the price could simply be a marketing strategy. Maybe they bought too many to sell. Maybe they are trying to clear up warehouse space for something of more value. You just cannot tell. The name Asus is a reputable name, so as long as it isn’t reconditioned or reserviced or previously returned by another customer, it should be fine. The only problem is that the extra options and accessories always have a hidden price of headaches in troubleshooting and compatibility. It will work, it just may be a headache.
In case you don’t know, RAID is a form of data redundancy within your computer, and only works if you have more than one hard drive (not partition). The Firewire is the high speed USB that Apple invented. It is used mainly for video production and that sort of high bus speed necessity activities. Plus, the two extra USB ports can’t hurt.
All in all, I doubt that you will use all of the extras to their full potential. Some of that stuff is server level stuff. It will all work, but read the manual. And if you don’t know what you are doing, choose “Reset Default Settings” in the BIOS.
But most importantly, try to order the computer case and processor assembled with the motherboard, even if there is a slight manufacturing cost involved. That will insure that the computer was properly manufactured, maybe quickly tested, and at least worked at the warehouse.
