When I add a new component to one assembly configuration, it appears in all of them. Why?
This behavior is due to the default settings for assembly configurations. These settings can be changed on the fly for existing documents, and also changed and saved to your favorite Assembly Document Template for future documents. Then, components added in one configuration are automatically suppressed in other configurations.
1) Create a new assembly.
2) Activate the ConfigurationManager tab at the top of the FeatureManager.
3) Right-click on the Default configuration and choose Properties.
4) 2/3 of the way down the dialog box, notice the grouping labeled "Properties for Newly Inserted Items". This group contains three check-boxes. The setting to Suppress Component Models should be checked. Once you check this box, components added in other configurations will be suppressed in this configuration.
5) Turn on this checkbox in your new assembly and then choose File - Save As - Assembly Document Template (*.asmdot). Save over your default template, and assembly configurations will have a more intuitive behavior.
Note: For existing files, you will need to turn on this checkbox for every configuration of every assembly if you want this behavior.