The way I understand it is that all mass comes from the force that joins the quarks together since empty space is not really empty and in case of a proton the particle is made of three quarks two up and one down they actually use up energy to create an empty space between them seeking "equilibrium" and since the energy that holds these particles doesn't just go no where it translates into what we call mass and this justlooking at the it ismatter this way explains how mass and energy is just one thing that is looked at from two perspectives, adding to that the weight (really small) of the quarks which is created by the "interaction" of the higgs field with them and can be looked at as if the quarks were metallic balls and the field is made of honey which doesnt make the balls stop but they doent go full speed either.... hope I helped :)