How many bags of ADA Amazonia Soil II do I need for a 12 gallow bowfront tank?

Three inches of substrate is an extraordinary deep substrate, especially for a freshwater planted tank. If this was a cichlid tank I wouldn't be worried since many cichlids tend to do their own rearranging of the decorations on their own and pockets of anaerobic bacteria won't spring up. In three inches of substrate even with plants you could have that trouble.

I'm looking at my six gallon eclipse right now. I used a single bag of amazonia and I've got roughly an inch and a half depth(three liter if I recall). The tank is heavily planted and all I use is Seachem's Flourish excel as an extra fertilizer

Given this is a six gallon tank and yours is twelve, I'd use two bags(three liter bags, or one six liter) for the same level, though for 3 inches I would guess atleast one nine liter bag.

I would choose the 9l bag, it may be expensive however you should have some left over which you could use for another project. For more information visit http://www.adana.co.jp/index_e.php