The ideal is for the bullets from the top barrel to be striking above those of the bottom barrel, by about the same distance as the distance between the muzzles.

The first thing that needs to be checked is the way that you are shooting. You may be aware of this, but to check the regulation you need to hold the rifle as you would in the field. In other words, in your two hands, not sitting it directly on a rest but resting the back of your weak hand while holding the fore end.

Next you need to see where each individual barrel is printing, which can be done by setting up two targets, and firing the bottom barrel at the first and then the top barrel at the second, one after the other in short order.

If the bottom barrel is printing low and the top shooting high, the usual cure is a faster load. If instead they cross, with the bottom barrel shooting higher than the top, the usual cure is a slower load. And if they are separated horizontally you may find it is due to canting the rifle.

a composite group of 3" at 90 yards should be achievable. FWIW my own much more utilitarian double shoots 4 shots (2+2) into about 2 1/2" or so at 100, scoped.

HTH