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since 50Hz is below the XO point for sub out on the EQ, 50Hz will affect the sub out, and mostly the sub out only, aside from some slight roll off that may catch the lower range of your mids.
I'd suggest you a: add bass blockers, or 2nd order high pass filters to your mids, and then b: re-tune your system eliminating all bass from the mids, and letting the sub handle all of that.
then you won't get the popping in your mids, and the sub can do it's job as it was meant to do without the rest of the system suffering.

I have a question concerning my Clarion 7 band graphic EQ, it`s doing what I call "channel blending" the unit is only 2 months old, When I first installed my system the dual voice coil Cerwin Vega 12 was doing it`s job, over the past weeks I noticed the bass response getting poorer and poorer, I suspected the EQ was doing what every graphic EQ I`ve ever owned was doing. the EQ has a seperate sub volume and it`s crossed over at 90 hertz, I keep the 50 hertz slider on the 7 band section almost at it`s lowest setting to keep my mids and highs from popping and distorting, today to test what I thought was happening, I moved the 50 hertz slider to half way and it may as well have blew the trunk off, the thing really went to hitting like a sledge hammer, I turned the sub volume all the way down and the sub went quiet as it should and the rest of the speakers played fine, Next I turned the sub back up and moved the 50 hertz slider back down to zero and all the bass went with it on the sub. when I first got this unit it didn`t do this, the 7 bands had zero effect on the subwoofer channel, now they do and it makes no sense at all, as I said, every EQ I`ve ever had did this but not when new, they always did it after a month or so use, can anyone tell me what causes this? I call it "channel blending" as I don`t know what else to call it, and is there anything I can do to fix it? if not I`m just going to throw the thing away and likely go with a digital unit.