To clarify my question. An example would be if I had a box with a 4" shaft coming out of it. The box would be a part and the 4" shaft would be a part. Now, lets say I wanted my shaft to be 8". Instead of making a new shaft with a new part number, I would make a configuration. My question is, when I make the configuration of the now 8" shaft. I wouldn't want the 4" shaft to change size. I want two different assemblies with two different shaft sizes. But, when I do that, my 8" configuration changes the size of the shaft in all assemblies. How do I get that to not happen?
Make sure your part configurations are actually different. It sounds like you made a new config and went in a changed the dim. That will actually change all the configs if you do it that way. You need to use a design table or different features.
When you right-click the part having different configurations in an assembly the topmost option shows the current configuration of that part. From that dropdown menu, you can select the configuration you want to keep for that specific part.
There is no problem in keeping multiple version of the same part with different configurations in that assembly