There are only 2 ways to link a test to a configuration...either 1. select the test (or test set), open the link to items, select the configuration folder, and check each sub item (e.g. Windows8>IE,...
I agree this needs to be improved. There are several things like this in QAC that require hundreds or thousands of clicks/steps to complete which as OP pointed out a lot of overhead and incredibly inefficient. A select all as one poster mentioned would be an improvement but there are other modern UI workflows that could make this better.