I don't see that there is anything wrong with placing batteries above each other as long as the materials used for the mounting are fab'd to carry the weight and the TT tongue can support the weight at that location. My thought is how you decide which battery set up to go with, hopefully you are comparing Amp Hours (Ah) of the two 6's vs the 12. If you are getting enough additional Ah with the 6's to get through your camping plans over the 12 and at what cost. On a small TT one 12 and a generator will make sure you don't run out of power while camping this time and on future perhaps longer outings. I recently went though the same decision process myself except I was deciding on 2 - 12's vs 4 - 6's, I went with 4 - 6's and 288 watts of solar on the roof of my 26 footer Wildwwod T26TBSS.
Whichever you decide I wish you well and happy camping!!
Dale & Terri, Lulu & Tiki (our Chihuahua's), New rescue puppy Prince - Pom/Pug mix.
2013 Tundra, Double Cab, 5.7, TRD Off-Road, 4X4, Full Tow Package
2013 Wildwood T26TBSS - Sold
2000 Gulf Stream Sun Voyager M-8357 MH, Ford Trident V10 Gasser, 35 foot.