When upgrading to a higher output alternator you should always install a larger wire between the alternator and battery. Even with a standard output alternator you will get better performance and life out of your alternator if you upgrade the main battery wiring. The original wire just isn't large enough for proper power transfer. If you are using your alternator to it's maximum output or when you upgrade to a higher output Alternator you must increase the wires size. An alternators ability to send the power it is making to the battery is directly related to the wire size and quality of connection between the alternator and battery. Also, a wire that is to small when used on a high output alternator can cause the power to back up within the alternator making it overheat, burn up and fail.
Another area that little is paid attention to is the ground. You must also improve the ground as well. A poor ground will hinder the alternators ability to send power to the battery and can burn an alternator up just as fast as an inadequate alternator to battery wire. Your ground may be fine when you first install your alternator but over time corrosion and resistance builds up in the ground connections. This is why it is best to run the ground directly from the rear of the alternator to the battery.
Here is another great auto electric tip from National Quick Start Sales on upgrading the wire between the alternator and battery. Randy says, you do not need to rip out your old wiring when upgrading. You can piggy back a second wire between the alternator and battery. The main battery wire connected to the back of the alternator has power to it at all times, even when the vehicle is shut off. You connect this wire like normal then you run a second wire between the alternator and battery. The power coming out of the alternator will treat the two wires as one, power follows the path of least resistance.
On a safety note, when running the second wire you should fuse it near the battery. The fuse is just in case the wire gets pinched or shorted out, the fuse will blow instead of the wire burning up. You should use the largest fuse you can for the wire size, fuses are restrictive to current flow. Typically you want the fuse value to equal 80% of the wires load carrying capacity.