I am a relatively new owner of a pre-owned Handiquilter 16. There is certainly a learning curve. I too have found the Superior threads website to contain valuable information.
I've had the best luck with Bottom Line (I buy prewound bobbins) in the bobbin and either Bottom Line or So Fine 50 in the top. I've used King Tut on top but it is harder to get right. I'm assuming it will get easier with experience.
Btw, you can get a wonderful selection of colors, including variegated, in poly.
Good luck! When all goes well, it's a dream!