Personally I detest using invisible thread and my Berninas don't like it much either. I managed to break one of my Viking bobbins(plastic) winding invisible thread on to it.
I much prefer cotton threads.
Just my 2 cents.

How can you secure the invisible thread when starting and stopping? If I sew two or three stiches in place, I get little knots.

i was having same problems with invisible thread so i checked with my local quilt shop today and they told me to lower my upper tension, use cotton/poly on bobbin, place my spool on tall thread holder fastened to back of my machine and go SLOW! Solved my problems

I use invisible thread for quilting alot. Since I am not that good at machine quilting it hides alot. Sometimes if the thread is old it doesnt want to work. I have used it in the bobbin but once in awhile it breaks and you cant find it. Also a metallic needle can help plus putting it on a spool pin thats not sideways helps. Jean

Lots of good answers already. Do remember that not all invisible thread is created equal. I like SewArt Int. (nylon) because it has a matte finish. Superior's Monopoly is great and the Sulky Polyester invisible is also pretty good. Haven't used YLI or the others, and avoid the stuff that feels like fishing line. <G>
Do be careful when you use nylon invisible. It doesn't stand up as well to heat. Story: I used to work as an alterations tailor in a major department store. We used an industrial blind hem machine and gigantic cones of nylon invisible thread to hem pants.
Someone came in and needed the hems put back in their pants because the thread "disappeared" in the dryer. <G>

So it can happen if you aren't careful.

But I do love using invisible to quilt with for all the reasons given.

Have fun,
Pati, in Phx

What brand of invisible thread are you using? I had trouble with Coats & Clark after they went to the new pink spools, the thread will wind itself around the thread spindle, and tighten and break. I have switched to YLI, on a spool shaped like a little silo, a little more expensive, but has 1500 yds on the "silo", and doesn't have that problem at all. If you have a lot of C&C spools that cause problems, I found a product called Baby net, that is netting to use on cones of thread. They are long, so cut one in thirds, and slip over the thread spool, and it will stop that annoying breakage.

Sie

Ohhh, good idea on the thread net, I hadn't thought about that.

You might try using "lingere" thread in the bobbin. I use it when playing with the shiney Sulkey sliver metalics. There is some give and there is less breakage. It has a soft feel so is soft against the skin hence, lingere.

First invisible thread I used was Coats and Clark and had nothing but breakage. YLI works fine in my Pfaff, either in the bobbin or on top. First I do trial stitching runs on a quilt sandwich using the backing and top fabrics and batting until I have the stitch length and tension I want. May in Jersey

PS. Like the idea someone posted about unthreading the invisible thread into an ashtry to get the kinks out, sounds like a good idea.

Call where you bought your machine and they will tell you what to do. For my Bernina I just turn the tension to 2 and have no problems