i use a lot of out door organic garden soil, and i have had my share of problems with fungus nats small centipeeds ect, i recomdend 2 things for you.
1. cover the top of your soild with 2 inches of sand, this will Help prevent bugs from living in your dirt
2. get your self some doctor dooms, works well and seems to do very little to no damage to plants, and this will kill most pests you will encounter with indoor growing.