You can run your complete model including your control variables. The role of control variables is to control their effect in the model so the error term is not affected.
While running the GLS random-effects (RE) model or fixed-effects model, control variables should be included alongwith IV & DV. Control variables are usually variables that you are not particularly interested in, but that are related to the dependent variable. You want to remove their effects from the equation. Inclusion of control variables removes the effect of such variables so that error term is not inflated.