You don't soak seeds in neem oil period. If you have fungal gnats then it's not the fault of the plant or the seed. It's your fault for not having a clean grow area (if indoors, outdoors not much you can do) or it’s your fault that you are over watering. (the most common cause of fungal gnats)

To help keep the plants healthy and stronger you can ad some barrier & silica to your feeding schedule to help keep the pests away and the plants healthy.