I too have the Janome 6600 and love it, especially for FMQ as it has such a good sized throat. One thing I will say with the loops on bottom problem is that that is a tension problem. Try sewing in a straight line - do you have loops then? If you do adjust your top tension a little until the thread is even top & bottom. If you don't have loops when sewing straight then you have moving your material too quickly. Something we are all guilty at times especially on curves of any sort. Think of it like driving a car - slow down for the corners! Hope this helps.
Jan