You might drain the trans fluid in the above mentioned way until the fluid level in the trans is low if you want to get as much dirty fluid out as you can,but I wouldnt like to let it run until its completely empty, as its probably not good for the transmission to be ran dry of fluid...Its best to just drop the trans pan and drain the fluid.And if the auto fluid is fairly dirty,then change the filter and fluid again for a second time in a few weeks first up, then again once every couple of months until its clean.
I change my auto trans filter and fluid every 4th engine oil change or every 20,000 k's in my VSV6. I drive it fairly hard,I shift it like a manual a lot etc, so I like to keep it serviced regularly. Its done 180,000 km so far being driven like this, and it still runs and shifts etc as good as the day I got the car. A lot of people will bag these autos and say that they are rubbish etc etc, but so far Ive found that they arent too bad under fairly hard use, as long as they are serviced regularly, and as long as a good auxilliary transmission fluid cooler is used to keep temperature out of the trans fluid when its under hard use.
Another thing is how many people have no idea how to let an auto upshift under full power/full throttle without having it slipping unnecessarily on the upshifts, which just kills autos in no time when driven in this way. Its always best to let the transmission get the shift over and done with as quick as possible, even if that means backing off the power for a split second to help the auto complete the shift properly before the trans is put back under full load again in the next gear.If driven properly and looked after service wise,these can be a fairly reliable transmssion.
One last thing I will mention is making sure the auto transmission is fully up at operating temperature before running it under full power or high speed etc.This should go without saying anyway to most wise people on here,as most people who drive their car hard without first having the engine/trans up at operating temp, usually have no idea what they are doing or the engine/transmission wear etc they cause by doing this.Its best to idle the car along slowly and just cruise until its fully warmed up,then get into it if you want.Your cars engine and trans will usually last a lot longer if treated this way..