When putting my character model's jacket over their shirt, it causes the clothing to shake around. Why is this happening and how can I fix it?

More information please.....

When you say 'putting .. jacket over...shirt', do you mean that you are sewing the jacket together, over an completed shirt. Or are you adding a completed jacket to the scene over a completed shirt, and during the sim, the clothing shakes? What kind of shaking is happening?
The program has a lot of calculations to make to keep the cloth in it's proper position, and some movement is to be expected as these issues get resolved by the calculation process. But the cloth should settle down eventually.
If your shaking is lasting a long while, or if the cloth mesh of the two garments tangles themselves into each other, that is a genuine problem. But more information would be needed to solve it: What layer settings were you using? Are the normals of each garment pointing the correct way?
Many questions.....Screenshots help.

Simulations that do not settle are pretty common. A few things to check:

1 -is there enough space inside the jacket? Most common beginner's fault is they do not yet appreciate the importance of room or 'ease'. Take a jacket that fits you well over a shirt. Measure the circumference of the sleeve and compare with the circumference of your arm at the same location. This gives an idea of the space needed. Do same for circumference of chest.

2 - are all normals pointing the right way (to outside)? If the shirt is folded there are vertices with facets pointing inside that push your jacket verts the wrong way.

Typical approach for layered garments: drape and freeze layer by layer, starting from the body. Make layers not yet processed inactive and invisible.

@RoseMaryR I'm trying to sow together a jacket over a completed shirt, and during the simulation, the clothing shakes on and on endlessly. The shirt and the jacket actually swap back and forth between which one's shaking.

@FVerbass There should be enough space inside of the jacket. I thought that there was, anyway. I'm not sure how to go about finding that out, though.

The shirt isn't folded up/back or anything, so I don't think it should be messing with the normals. There are creases/wrinkles, but I wouldn't assume that that would cause a problem, either.

A screen shot will help us understand the isseu better.

as said freeze the shirt patterns. You can then build the jacket on that.

You can also assign a layer number layers to the patterns. There is also the layers mechanism. It is not infallable but more reliable than the superimpose over/under.

The Superimpose function should be used on a single garment when there are two or more layers of cloth sewn together, such as a double-thickness waistband, or a button placket on a shirt, or pocket.

Layers should be used to keep two or more different garments in their correct positions, such as a shirt tucked into a pants, both of which are covered by a jacket. And after the layers are acting correctly in simulation, they should all be reset to the zero layer at the end.

I already tried to freeze the shirt and then place the jacket over it. The same problems occured.

Could you further explain the difference between the layer numbers and the layers mechanism? I did try assigning to layers, but I still got the same problems.

Default layer = zero That one is next to the skin of the avatar.

Layer 1 is the next one out.

Add an incremental number for each garment stacked on top....

For example: Shirt (which is tucked into pants). Shirt should be at Layer 0 in the Property Editor, pants should be at Layer 1.
Run your sim, make sure they settle into place, then select all the garments and reset all of them to Layer 0, before adding another layer for simulation.

The program 'learns' which mesh should be on top of which other mesh(es).

Yes, this is what I already attempted, yet I still get the same shaking results. What else can I try?

Can we see a screenshot, please. Include both of the 3D and 2D work areas, and the Property Editor area. We need more information about the entire setup.