One filter is in the suction line to the main oil pump driven by the engine. The other is for the Hydrostatic transmission, if your tractor is so equipped. Hydrostatic transmissions operate by means of a hydraulic motor driven by pressure from the pump on the engine. Hydraulic motors are more sensitive to debris than are cylinders, and the filter for them is typically a much finer filter than what is typically necessary for a cylinder, e.g. the lift, or the FEL (if equipped).
More plainly, the Suction filter cleans all the oil leaving the transmission going to the main pump. The HST filter cleans the oil coming from the output of the main pump. The discharge of the main drive hydraulic motor goes back to tank/housing