Hello,
I believe that it is right that there is no difference in the model, however, there is a difference in how they are placed in the design matrix.
The covariates entered under the design specification are always first in the design matrix while the ones entered in the 'multiple regression' heading come after. So if you entered A1 and A2 in the design specification and B1 and B2 in the multiple regression heading the order would be A1, A2, B1, B2 in the matrix.
Otherwise I don't believe there is a difference. However, I do use it for organization purposes. I'll put covariates of interest under the multiple regression heading and covariates of non-interest under the design specification heading.
I hope that people will speak up and correct me if my assumption that there is no difference in the model is incorrect.
-John
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