You can but I don't know what the results would be w/o knowing the cooler and the MoBo. For one, i don't know whether your SYS header is PWM or DCV. Just because it's 4 pin doesn't necessarily mean it's PWM. Again, you didn't anser as yo what CLC you were considering. Frankly at $50 there is no CLC / AIO that can compete with air coolers in that price range like the Scythe and Phanteks .
At $50 price range ($55), I'd use this
http://www.newegg.com/Product/Product.aspx?Item=N82E16835709004
http://www.newegg.com/Product/Product.aspx?Item=N82E16835709002
It comes with a PWM converter and a splitter for the two fans and it will be bothy quieter and cooler than any 1 fan CLC with a 2nd fan added.
Your sys fan header will remain...