Thomson's experiments with cathode ray tubes helped him to discover the electron (which Dalton did not know about). Dalton thought that atoms were indivisible particles, and Thomson's discovery of the electron proved the existence of subatomic particles.
This ushered in a model of atomic structure referred to as the plum pudding model. I like to think of it like a sphere shaped chocolate chip cookie since plum pudding is not super popular in the US.
The cookie dough (they didn't know what it was yet) is positively charged and the chocolate chips (electrons) are negatively charged and scattered randomly throughout the cookie (atom). The positive and negative charges cancel producing a neutral atom.
Later discoveries by Rutherford and others lead to additional revisions to atomic theory.