Lots of questions in there John but I'll have a shot.
USB. I'm guessing the atik wheel has no power source plugged in apart from the USB. USB only supplies .5amp and if you run that over a 5meter lead you will have a voltage drop. So you where probably getting low volts to the wheel. Now it's on a powered hub the voltage drop is gone.
I normally shoot colour at 2x with 1/2 the exposure time. So 10 minute L @ 1x1 and 5 minute RGB @ 2x2.
Use the mask and focus on a star with L then rotate the other filters in and check they are all in focus (parfocal). For bloated BG, check the filters are the right way round in the wheel. Imagine no wheel and they should be sitting the way round you would normally screw then into the nose. If they are right way round, try a light pollution filter in front of everything, that solved all my bloated star problems.
Colour mixing ratios are established by doing a G2V star calibration. Search for that one.
Sometimes I just combine and stack them as is, other times I'll de-convolve the L and other times de-convolve all sets. I find mixing in Ha kills the colour but you can up saturation in photoshop to compensate. Trial and error is the order of the day till you get a flow that works for you. I've found DDP stretching helps me a lot at times and other times it destroys the image
