Welcome to Librarium Online!
yo, i was thinking of starting a Witch Hunter army, i was thinking of starting off with 2 troop choices (So and an HQ, but i dont know which HQ to take. I also have 5 Grey KNights i might include later on, but i want to keep my army mainly Witch Hunter related. Also does it really matter which order u choose, like order of our martyred lady, etc., or is it just mainly for fluff?
the orders are really just there for fluff and paint scheme. Its not hard to invent your own order if you like though.
Sounds like you have a good plan so far. For HQ I recomend Cannoness. Only because she doesn't need a retinue like the Inquisiter Lord. As an army your just starting, it makes sense to reduce the number of minis you need.