Honestly the stuff works great and almost feels like aheatsink in itself. I did the same thing on a cheap airplane ESC and the thermal epoxy worked great for not only water-proofing the esc, but also pulling heat from the ESC as well. It should work great in this application.
What did you use, and where did you find it? I had almost considered using jb weld, but I do not know if it conducts heat very well. I hate to buy this stuff in tiny syringes.. Larger quantities would be nice!