yeah i have a 6 gallon fluval edge that has a betta and established HOB filter. i just put in power soil, new amazonia [regular and powder]. The first day i did 100% WC, with some re-scaping. second day, 20% and then today another 20%. before the WC today i tested ammonia and dropped drastically from the first day - so no doubt an already established media filter is doing some work.
I personally would keep up on your WC's if you add your betta back into the new environment. (maybe 10% every 12 hours) or test it daily.
worst case scenario, get a holding tank (a clean gallon bucket) fill it and just have a refuge their for him till you are certain the NH is gone. (i personally have mine is a 1 gallon fish bowl, doing 20% WC's. I know he is pissed at me *sighs*)