I'm not quite sure what you mean with the store.config file. DNN Store.dnn.config is used once during the initial installation of the store module within DNN, it describes the files that need to installed.

You can add your new tax provider by copying the files and file structure found in Store/Providers/TaxProviders/DefaultTaxProvider, then add your .dll to the bin folder of your DotNetNuke site. Note that multiple tax providers do not work in version 1.0.1 so you will have to replace the files within the DefaultTaxProvider.

When you select the Store Admin module it will use your new files.

I hope this is of some help to you.