Yes, matching the bobbin and top thread is very important because those threads that poke through to the top are very distracting and ugly:< I have to disagree that laundering it will make them disappear. I've not had a machine yet that I can put a different color thread in the top and bottom and not get this occasionally. You can play with the tension and get it just perfect and then do a quick curve etc. and see the bobbin thread pulled up. Not attractive. So, yes, it's easier and less hassle to use the same bobbin and top thread at the same time.

I had wondered about this, too...I usually will end up matching the bobbin thread to the back, especially if dark backing...now, sometimes I have gotten small "pokeys", but in my opinion, I am not good enough with the fmq to have my back thread show up as bright as white thread would on black fabric...I also will just hand quilt, I like that anyway, and that way I can control my stitches...just boils down to what you like, and what you are comfortable with...good luck,
K

Another thought...what about a clear thread. I've used Superior MonoPoly for top and bottom when I am quilting over many colors and value changes. It doesn't melt with the iron and hides lots of sins...in case you make any.