The wider Q factor of a fat bike can lead to serious knee issues. I've been thinking about what I did wrong on my fat bike last year and I thought I might share my mistakes. You can do what you want with the information.
Fat bikes are a lot of fun and you should ride yours. But not as much and not as hard as you do your summer bike. Make sure to transition slowly to the fat bike. And when you do fully transition, just have fun. This is the off season; you don't have to make every ride a suffer fest. A fat bike is made for floating on snow, not for perfect body mechanics. Your mechanics are compromised by the wide BB, so doing hard efforts every day might be doing more harm than good.
Get a crankset that is as narrow as possible. Look at the gap between your crank arms and chainstays. If there is more than half an inch, get some narrower cranks. My gap was almost an inch on each side. Therefore, my Q factor was two inches wider than it had to be. Even going as narrow as possible, the Q factor of fat bikes is less than optimal for most people. I think the e13 crankset is about as narrow as you can go. Spend the money. And slide your cleats laterally until your shoe rubs on the crank, or damn near if you're concerned about scuff marks.
Shoes, shoes, shoes. You're already on a bike that is totally different from what you've been riding all year, and to make matters worse you're slipping into different shoes as well. Most of us wear the Lake winter boots. These are awesome, and toasty warm, and that Boa system--awesome. But take a look at the insole. Go do it right now. There isn't one. It's a piece of insulation, flat as cardboard. Why does this matter? Pronation. Pronation is what happens when your arches aren't supported. It causes your knees to be pulled out of alignment. Instead of a straight line between hip, center of patella, and second toe, the line will kink at the knee. Pronation pulls the knee joint in towards the top tube. The wide BB of a fat bike, combined with no arch support will conspire to kill your knees. The wide BB is already pulling the knee in towards the top tube; and flat insoles cause the knee to drift even further out of alignment. This is easy to fix, however. Leave the cardboard in your Lakes and put your summer insoles on top. But if you've got an extra 125 bucks, go see Balser at Penn and he will set you up with some custom molded insoles. They will not only save your knees but more importantly they will make you faster.
Pedals. Hmmm. I don't know a lot about pedals, but I know that crank brothers suck. They should be avoided at all costs. Sure they look cool and the don't fill up with mud or snow, but the engagement is so sloppy. This is particularly a problem with the Lake boots because the tread isn't as tall. To see what I'm talking about, try this: clip an empty shoe into your crank bros. Notice how you can rock the shoe side to side. Notice how you can slide the shoe fore, aft, and side to side.This is slop, and slop is bad for your knees. Slop should not be confused for float. If you have speedplay road pedals you know what I mean. This is what pedals should feel like. They have perfect, slop-free engagement, and the smoothest float you've ever floated on. But you can't ride speedplays on your pugsley. Or can you? I heard Speedplay is coming out with a new mountain pedal this winter. They might be available already, I don't know. Anyways, they're supposed to have the best engagement in the world. If I were you I would look into getting a pair of these. If you must stick to your crank bros, there is a trick to get rid of some of that knee-killing slop. Wrap a bit of athletic tape around the pedal where the shoe lugs contact the pedal. Not too much though because you don't want to eliminate all your float.
Lastly, I can tell you that your adductors (your inner thigh muscles) are going to get really tight as a consequence of riding a fat bike. You wont necessarily even feel it. But what will happen is that those tight muscles will pull your knee even further in towards the top tube. All you have to do to prevent this is stretch. http://www.youtube.com/watch?v=7aM7ezL1rpU&feature=related Here's a link to a basic adductor stretch. I like to support my weight on a chair while I do it. And don't be afraid to hold it for two, even three, minutes. Like I said, this is a basic one, and you will find a lot more when you google "adductor stretch." If you have a foam roller, you can use than on your adductors as well.
So in review: Start slow, get a new crank, get some decent insoles in your boots, throw your crank brothers in the garbage, and don't forget to stretch your groin.
Hope this helps you stay injury free this fat bike season.