Bart, it is always best to apply decals to a smooth gloss surface. If you require a flat finish, then use a flat coat afterwards. The reason for this is that a decal may not completely adhere to a flat finish, and what can happen is that the light goes through the clear carrier and then bounces off of the model and then it hits the back side of the clear carrier. This causes a "silvering" effect.
As far as the yellowing, it kind of depends on what caused it. Some decals like paper can yellow with age. If this has happened I am not sure what you can do other than what Snake suggested. The other thing that can happen with older decals is that the glue can age an cause this problem. You can see this on the race car above. If this has occurred, there is likely nothing that can be done about that.