Thru a lot of trial & errors I've finally gotten it down how to set my machine (Brother) and I have no problems, I've been quilting Christmas Wall Hangings all week & it looks really good. I cut the thread long, thread a needle then bury it in the batting & you don't have sharp ends.

I've always been told not to use the invisible thread in the bobbin. ??

Hmm, I don't know why. In fact, often that's where I want the "invisible" part, and nobody told me I couldn't... It's working for me.

I LOVE invisible thread. I have only used Sulky so far and have not had a minute of trouble with it. When I applique with it, I set it on the upright spool holder, use size 60 Sharp needle, adjust my upper tension to 2.5 on my machine and use it in the bobbin (half full) and applique away. It works great for the invisible machine applique method, especially that I don't have different threads to match all my pieces, so invisible to the rescue! I have occasionally used it for quilting (especially great for STID) and use a size 75 quilting or top stitch needle for that. A teacher at a LQS told me once and she personally recommends YLI for people who have troubles with other brands on their machines, she said she's seen a lot of success with that brand on different machines. I wouldn't know, never used it before.
Do show us those blocks :)

It should only come off the end of the spool if it's a cross wound thread. If it's a stack wound thread it should come off the side of the spool. I don't think I've seen an invisible thread that is a cross wound. It's easy to tell the difference between cross and stack wound spools. Cross wound crosses over itself and stack doesn't. Most invisible thread behaves better if it maintains a little tension as it comes off the spool. When you let it come off the top of the spool and relax it gets unruly and starts twisting up and pooling around the bottom of the spool.

I have a Viking and I use the brand that my dealer carries. Love it.
The only problem I have is seeing the invisible stuff to thread the needle.
The older my eyes get the less I can use it. :(

Since some of it stretches, it will wind too tightly on the bobbin and make it extremely difficult to get the bobbin off the winder. Been there..done that! It can be put in the bobbin but keep a very close eye on the winder and again, it really depends on the brand & type of invisible you're trying to use. Wendy must have one of the "tame" invisibles.

What brands of invisible thread are the best/easiest to use? Any suggestions/recommendations?

I use invisible thread on the TOP only when doing SID. I really like it since you can not see top stitching and therefore your mistakes. I use regular thread on the bobbin and it gives a nice pattern on the backing. I have tried FMQ with invisible thread and do not like it. I need to put thread in upright position either in holder on machine or in a cup. Also you need to sew slow so thread does not "whip". Keep trying and you may learn to like it.

I must agree, I DO NOT LIKE invisible thread. I just can't seem to get it to work properly.