Hello Fernando,
Matt already mentioned to this, but while removing contamination using controls sounds easy, it's really hard to do well and has unintended consequences. Be careful! 
Yes! The qiime quality-control evaluate-composition plugin comes to mind. Let's see what @ebolyen recommends.
Or maybe you could treat your controls like a treatment group. In this method, you keep all your samples in your cohort, but when you perform statistical testing, you pass Treatment (channel wash control vs real sample) along with your main biological categories. When you get the results, you will be able to compare the effect size of biological differences like pH, timepoint to the artificial differences (channel wash control vs real sample). Plugins like qiime longitudinal should elegantly support this.
Let me know what you think! I'm also curious how @ebolyen would make use of matched negative controls. 
Colin