If i'm correct you said you already punched the holes in your bottom piece. Form your gusset with extra leather for trimming, glue your two pieces together then you will have to punch through the existing holes on the bottom piece with an awl or some such, sew it together then trim the edges straight. Thats about the only way i can think of fixing your problem. You can pre punch leather if you are using a pattern and diamond chisels but even then its ify especially of wet forming.