It looks like, going forward, you should be using your Qantas-points-earning credit card and accumulating Qantas FF points to add to the 100,000 you already have.
As for your Altitude points and AmEx points, those points will never end up as Qantas points*. You can’t convert Velocity or KrisFlyer points to Qantas points. Whether you transfer them to Velocity or KrisFlyer will really depend on how you want to use your points. If you mainly want to use them to fly domestically with Virgin, or if you don’t think you’ll use them within 3 years, then Velocity is probably your best bet. If you have international redemptions in mind on Singapore or other Star Alliance airlines, then KrisFlyer may be best for you. Don’t transfer them until you know what you want to do with them, lest you transfer them into the less-than-optimum FF programme for your needs.
*There is one fairly complex, risky and potentially-expensive “hack” which might mean that you can transfer your AmEx points to Qantas: if you get an AmEx Platinum card, whose points (called “Ascent Premium” points) can be transferred to Qantas, you could then call AmEx and politely ask if your existing points can be transferred to the “Ascent Premium” points category. If they agree, you could then transfer your AmEx points into Qantas. But be warned: the annual fee for the Platinum card is over $1000 so do your own due diligence and get your own advice regarding whether it’s really worth the expense.