I, too, put the spool in a small container behind the machine, directly below the spool spindle.
I also tape a closed safety pin upside down (loop end extends beyond the top of the machine) to the back of the machine and thread the invisible thread through the "loop". The loop acts a trolley that helps to guide the "thread" into the threading mechanism of the machine.
Once I discovered to do that, I have no issues with using the "invisible thread" as a top thread.
I haven't had such good luck using it in the bobbin (and that includes purchasing the "thread" on pre-wound bobbins).
Hope this trick helps.
m.