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The source term is applied to the cells, and heat generation is added into the walls. So, they don't overwrite and you could set both, which may be a bad idea. 

If you use a source term the fluid temperature will be based on source term and fluid residence time but the amount of energy added is uniform to the region. If you set the wall flux (or generation rate) then wall contact is a factor, so channels with low flow will get warmer. You could also set a source term on the solid parts: you don't say if the baffles are physically thick (ie a solid zone) or thin (just a wall & wall shadow pair). 

There's not a "best" solution in many cases, it depends on what you want to show in the model.