Deeper is better to keep more of the mutrients in the substrate longer IMO, but it doesn't really make a big difference.
They will slowly leach ammonium into the water regardless. In a heavily planted tank it's used up much more quickly than it could build up to cause any issues. I've had them pop up on me without realizing it many times, and haven't had any problems.
I personally use Multicote, which contains urea and ammonium. I was told by multiple people that it would cause all sorts of problems from algae to dead fish, none of which actually happened. It's a nice product because it has a thicker membrane and so should diffuse more slowly. I once buried probably 40x "00" capsules during a rescape at one point without any ill effects. I've used Osmocote brand in the past also.
I suppose the point of this whole reply is just to say that you should get them as deep as possible, but if you can only get them an inch down, it's not something you should lose any sleep over.