CAUTION! - THIS MODIFICATION WILL VOID YOUR WARRENTY!
These bags are great but the straps...well there are just too many! I couldn't makes sense of them so I cut off and sealed all of the MALE straps except the two on the front of the large bag (so, I cut off 6 in total). Leave the receiving clips alone!!! I took two of the long straps that I cut off and made them male/male (just use a couple of the male clips from the straps you just cut off the bags). Take a look at the photo of the rack on my tour pack. I simply crisscrossed the straps under the rack so I could secure the large bag to it.
I then placed the large piece of luggage on the rack and secured the M/M straps to the appropriate receiving clips. The bag was secure enough at this point to be able to open the pack lid with the luggage attached. Now, with the large bag secure, you should see the two straps hanging off the large bag that were not cut off (they should be hanging off the back of the motorcycle). Slide those straps under the rack and over the seat (see the photo with the view from the front). These straps will be used to secure the small bag.
At this point I took the small piece of luggage and fit it against the large piece in an upside down (inverted) position. I then placed the straps over the bottom (now the top) of the small bag, thread the clips through the strap guides, and secured the clips to two receiving clips on the back of the large bag. I just snugged up the straps and, voila, the small bag is secure!
That's it! As you'll see from the final photo, the bags don't sit too high and my wife has no problem with placement of the small bag. In fact, it provides some extra support.
Hope this helps.
p.s. Don't forget to seal the cut edges of the straps. I just heated a large flathead screwdriver over the flame of my stove and carefully drew it across the strap for a perfect seal. If you don't seal the cut edges, they will fray.