I am a little confused here. You do have a 3.5 with the 6F50 trans right? There should be a dipstick for checking fluid level. And yes, it must be checked with engine running, and trans at operating temperature (around 180F). This is why it is important to measure how much you drain out so you fill pretty much the same amount in, assuming original level before D/F was correct.
If you really wanted to change out the fluid, you could set up a continuous drain/fill so new fluid is drawn in while the old fluid is drawn out, and work through the gears while that happens, always ending in PARK. Do have to be careful to not let the new fluid bucket go dry, and use a deep pan for the old fluid.
The 6F35 does have a fluid level check plug/hole.