+1 on the sport rider settings
I must say, I disagree--somewhat. Remember, the 2006 has a stiffer spring rate than the previous years; when I set the suspension to the sport rider settings, I found handling was better, but too harsh. I carefully read and re-read Lee Parks' chapter on suspension settings in
Total Control, thought about it a lot, then on each ride paid careful attention to exactly what the front end was doing when it would hit bumps. And remember, there are two kinds of bumps, elevated and depressed, and the suspension should react equally to both, but what you adjust to handle each will be different.
As I rode for the first couple of thousand miles after setting the sport rider settings, I found that I needed to back off on both the compression and rebound damping in the forks a few clicks each to get a ride that held my wheel to the road. The goal is to have your settings such that when you hit a bump (either elevated or depressed), the suspension moves the wheel to just overcome the road hazard, without moving the handlebars. An ideal suspension would keep the mass of the bike at the same height relative to the road, moving the wheels under the bike to adjust for bumps. I found that the sport rider settings had too much compression damping so that when I hit an elevated bump, the front end would 'buck up'. Likewise, when hitting a depression, the front end would 'bob down' into the hole, indicating too much rebound damping.
In the rear, I found the same thing; too much rebound damping was keeping the suspension from soaking up crevaces, so I went a couple of clicks back. Unfortunately, the compression damping can't really be adjusted; I'm not sure if the lever is actually flipping between two compression damping settings, or just adjusting the preload (which only affects static sag), but I generally run it 'hard' for two up. I'm playing around with it on solo rides to determine if there's a big difference, though I do think it helps two up.
Backing off the damping front and rear has made my ride soooooo much smoother. When I tour two up and fully loaded, I do have to adjust the settings at the start of the trip, then move them back when I'm solo again. But figuring out how suspension works and what to adjust for various conditions has really helped. Go figure.
So be a scientist, make a single change, pay attention to how the handling is affected, and learn!