yeah for sure-- get rid of any old/contamniated grow media before you transplant. Assume the aphids are living in your old dirt, and as long as it is around (and for a few days after) you're at risk for root aphids. The fliers can live for over a week (and longer if it's cold), but I've found spraying/atomizing horticultural oils in the room between runs keeps them at bay, as does letting the room get as hot and dry as you can while it's empty (like, 0% humidity and 120 deg.) Aphids are most difficult when you have a perpetual veg- multiple plants in multiple different stages of growth. If you only veg one round of plants at a time it is much easier to manage them.
And yeah, as long as you've got the met and preferal in the pots you're good, i'd do an additional drench every week or two for preventative and if you see any aphids (even one) hit them twice a week, 4 days apart.