It is a very common mistake to think you can get away with using the second side of the fole to do the same stack. It doen't really work as whilst it looks similar it isn't exactly always the same.
What you need to do is you take your yardage which contains the number of fabric repeats you need. i tell my students to count a distinctive motif near or on the selvage. so if you are doing a 6 layer stack you need to have seven of your motifs to get 6 full repeats of the pattern. Take that piece and open it up. then cut (or you can tear if you wish) down the fold line. this gives you two lengthwise strips paralel to the selvage. take one of those and chop it up into your repeat pannels and stack those. The other half may also need to be stacked, but leave it in one piece until you are ready to use it. If you didn't need more blocks you can use that for borders etc, or you can share with a friend and split a nice fabric.
As you have gone so far, hopefully you have the rest fo the yardage you purchased. if so, take the second piece and cut it in half down the fold. Identify which side belongs to which panels you were trying to cut and cut enough to give you a full stack all containing the same edge of the selvage. try stacking those.
I LOVE stack N whack I even picked Bethany reynolds for a course assignment when doing my City & Guilds.
Hope that helps
best Becks