A friend of mine replaced the boots on his swing axle bug and said he didn't use any sealer, but they leaked . . . then someone told him they were installed wrong was the reason.
I would have assumed that the seam goes up, and that's the way I see most of them installed, but he says the seam should be pointing towards the back of the car. If it's up, it won't let the boot flex properly as the swing axle moves up and down and that's usually what causes them to leak.
Just remember though, I haven't done this. I don't know if the above is true or not, but it makes sense. I'd probably use a little silicone too, seems like it couldn't hurt. I need to replace the swing axle boots on my 63 bug someday . . . so if you figure out how to get them to seal, please let me know!