Touring - Am I loading my bike right?

I get the feeling that I'm doing this strange. Like there is a different way to pack the bike. When I look at the way I packed my panniers, I had all the clothing in one big pannier on the rear, with the bad weather in the opposite pannier. In the front I was loading the tools and pump and cook set. Just because I felt it should be that way. But in loosing a front panniers and a rear pannier I'm wondering if I am going about this all wrong. I know that's why we practice and work on loading and unloading until we get the right combination. I now wonder if I wouldn't have better success loading the panniers with the clothing etc up front, this would keep the panniers from making a lot of noise, and take some of the weight off them, and I'd have the emergency stuff up front, handy. The large panniers in the rear could have all the cooking and repair stuff in them along with the lesser used items of clothing.
How do you guys manage this stuff?

About the same way that you are!

The only thing that I would add is that if there is a heavier item in one of these areas I'll keep it on the bike side of the bag and as near to the bottom as possible to help with stability.

Otherwise how you have packed makes sense to you, so why change? What I mean is there really isn't a "wrong" way to pack until it gets dangerous for you to operate the bike.

Ride with it this way. If it seems awkward, make come changes to deal with the problems you are having. Also, how you pack may change as the tour progresses. For example, string of clear, dry days followed by some inclement days (or vise versa) might mean you would shift some stuff closer to the surface to deal with the changing daily needs. No need to have rain gear on top and in the way if it ain't gonna rain. There may be other reasons to move things around.

Heavy stuff. Yup, low and close to the vertical centerline of the bike for stability.

There really is no right or wrong way, but whatever way works best for you. I've been touring for years and I'm still searching for the best way to load the panniers. However, through trial and error I've learned the following:
1) Go ultralight. I ditched the stove and fuel in favor of food items that don't need cooking which I pick up at a store near my destination, or eat in restaurants. I carry only the most basic of tools for quick repairs. The major repairs happen far too infrequently to be dealing with carrying too many tools. If a major malfunction occurs, I let a local bike shop handle it, similar to what people do when a car breaks down on a trip. Of course, that's assuming your tour is in more developed countries or other locations where you can do it this way. I've also learned to travel without as much camping gear, such as a small sheet instead of a sleeping bag during warm weather touring, and a very, very small lightweight one person tent which I carry on the top of the rear rack.
2) How you pack may also depend on the style of your panniers. I have panniers with lots of outside pockets where I keep the things I may need most frequently or suddenly, such as my rain gear, jacket, camera, notepad, cash, etc. The stuff I use least I keep at the bottom of the main bag. Like you, I use a similar approach for packing each bag. I usually put my clothes in one bag and the other holds the housekeeping. Toiletry stuff I keep together in one small bag which I keep in the housekeeping pannier. I don't even bother with front bags anymore since I carry so little. It may not be the ideal balance weight distribution wise, but it works for me, and that is all that matters in the end.
Just keep touring and eventually you'll find the approach that works best for you.

If noise is the problem, the find some stuff to stop it. Like I mentioned the other day that I put my cookset (Trangia) into a beanie hat. Moving it to the rear pannier probably would help. Clothes in the front, sleep gear, cookgear and wet-weather stuff in the rear.

Ultimately, it comes down to what works for you when you (a) ride and get a feel for handling and the noise created by the jiggling (b) access to various needs such as snacks and wet-weather gear while riding (c) ease of finding stuff when you get into camp.

For me, all that is part and parcel of having fun on tour... the thinking process that enables you to come up with a better mousetrap.

When you lay your bike down it will likely be on the left side. Keep fragile stuff (if you have any) on the right side. Also, tools go on the right side so you can access them for your field repair.

Other than that, you are looking for left/right balance and a front/rear ratio that suits you. If you have low front bags you can put more weight in them and still keep stable. Trial and error is best here.