Apply a thin coat and use the short or wide end of an old credit card or something similar to spread it evenly out; best done in one pass. It takes a bit to get it right and you won't get it right the first time, but it is relatively easy to block sand any ridges out, you just have to do it slowly so you don't take one side down.
This application method is a common way to apply thermal paste to heat-sinks, so if you have done that then the JB weld is no different. If not it will take a bit of practice to get the hang of it. I have not done this on an AV bay end, but I have done it to several aft CRs as well as the bottom bulkheads of baffles, and it works well for easy cleaning as well as provides some thermal protection.