The designs that mainly benefit from having the speaker grill behind the light frames are the designs that have etched details in the designs or a large amount of etched area on them. Generally the more etched area there is in the design, the more important it is to get the grill from being between, or at least right behind, the design. EX: The LOTR design has the lettering detail etched in it. I prefer to have it mounted in front and the grill behind the light frame, but it still look quite nice with the grill directly behind that design. On the other hand, a design like South Park, Family Guy, the TRON cycles (SEE EXAMPLE) or Slimer (which is almost entirely etched) it is really important to not mount the speaker grill right behind the designs (SEE STEWIE EXAMPLE) as what you will see most is just grill dots in the etched area of the design. In the TRON example, you can see it's even hard to see the design at all with the grill mounted right behind it.
In the 4 picture Iron Man design picture above, the only difference between the 2nd and 3rd pictures is 2 washers were added on each of the 4 mounting points as spacers in the 2nd picture. Just adding that small amount of space between the back of the design and the grill helps to show more detail in the design and remove some of the grill hole pattern in the etched area. That being said, I think most will agree that the top picture (with the speaker grill behind the light frame) looks best in this case. Besides getting the grill from being between the design and the light source...mounting the grill in the back also makes it show up in the back of the lit area instead of the speaker. This gives it a much cleaner and less cluttered look.
As for double stacking the acrylic designs (1 acrylic design, then the light frame, then the 2nd acrylic design, then the speaker grill and the speaker), that actually looks good on a few of the different designs I sell. AC/DC figures in front of lightning bolts (SEE ATTACHMENT), Iron Man in front of Arc Reactors (AS PICTURED ABOVE), KISS logos in front of the face icons, spiders in front of webs, ect... This isn't anything I plan for when choosing designs. It is just something that sometimes works out when having different designs for the same game.
The best bet on getting these to look their best is to try different mounting orders with different designs to see what looks best to you. I try to point out the importance of the mounting order of the designs and Speaker Light Kits from time to time and how it can greatly impact the look of them, so I was glad to see this thread.
Doug (SpeakerLightKits.com)