I don't think you will find a 3.1 sound system. You could have a 4.1 sound system if your sound card supports 5.1 output. You could plug the monitor speakers into the front speakers output and the rear speakers into the rear speakers output.
Yes, just plug the speakers from the 2.1 setup into the rear speakers out, the monitor speakers into the front speakers out, and the subwoofer into the subwoofer out. Set it for 4.1 surround sound (use 5.1 if the option isn't available). The subwoofer is just one jack, and you will plug it into the subwoofer jack, or the center/subwoofer jack.
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