here is what I do, not saying its the best way, but it seems to have the best results, when transplanting, it's important to add mychorrizae directly to the roots, the best way to do this, is this, take the plant out of the container, spray the roots with a water bottle (plain water) the roots when wet will allow the myco to stick, so from there you sprinkle the mychorrizae directly on the rootball, cover the damn thing, keep an opened cardboard box under it and you can catch the excess myco to sprinkle on the soil too, most important is root-contact, I've noticed better results from this as opposed to sprinkling the soil.
If it's been a bit since the plant was in the soil, it may be a good idea to water with an aact prior to transplanting to allow the beneficials to colonize the container.