The standard proceedure is to add chemicals, tighten cap, agitate bottle thoroughly to evenly distribute Aqua Mira, hold bottle with cap at bottom, loosen cap slowly until a small amount of chemical laden water floods all the way around the thread area and flows over the cap's lip. Tighten cap and wait for chemical to do it's thing.
That's the easy part. If you have a narrow neck bottle, filling it is the trick. I carry a thin plastic picnic type cup for that purpose on the rare occasions that I'm not using a wide mouth bladder.