Just sew it... I have HUNDREDS of holes in my favorite pants. Two right under my junk. One hole for each!
Plus the gaping hole in the knee. If youre not going to sew the patches in, then it aint gonna happen. Or you could just walk around with the holes there. I wouldn't care if people saw my falling apart jeans. Actually, I dont, because i wear them all the time, and every single patch is noticeable. Just do whatever is comfortable man. If people have a problem with seeing your patches... fuck them, they dont have to look at your crotch.