Logan, I agree with the advice Gene and Tom have given you. Here are a couple of footnotes:
1. Once you guys get a lot of experience with this, you'll find that having 2 riders offers a great opportunity to apply the "sum of shortest splits" method of analysis that is explained in the manual. You compare both measurements of each mile and select the shorter measurement in your final summation. But using the overall measurements is a good way to start.
2. One exception to the advice to keep a good distance between you, just my opinion, is when this compromises safety. For example if you are using a vehicle behind you for protection from traffic, you don't want to be too spread out beyond that vehicle, or else motorists will just be roaring around you dangerously. But a little separation is also good for safety: last fall I was leading just such a double ride, in front of a car, when I suddenly jumped on my brakes, causing my measuring partner to crash and fall. Ouch, don't do that!
3. (out of 2): it's important to do lots of talking, letting each other know what you're going to do, making sure you're both on the same page as far as how the course is defined etc.