I just did my CJ7 tub 2 weekends ago... MAN, WHAT A PAIN!!!... but well worth the effort. The person I bought my Jeep from had done some home-made floor pan replacements using Aluminum -- did a pretty damn nice job of it. Just like you, he had also used silicon all the way around it, and the Herculiner didn't seem to have any problem sticking... although I wouldn't be too comfortable if I was covering large surfaces of silicon. As long as you have floor mats, I doubt it will be a problem.
Make sure you take your time preparing your tub. Applying the stuff is relatively easy, but if you don't properly clean and prepare the surfaces, it won't adhere as well as it should. Yeah, the stuff will stick remarkably well to your hands, clothes, feet, fingernails, etc... but it will eventually peel off of oily surfaces, improperly prepared aluminum, and even painted metal if you don't give it a good scuffing. I got some of it on my old seat bolts (which obviously had not been prepared), and two days later the Herculiner peeled off - as easy as the rind of an orange. Read the instructions (especially if you have any aluminum surfaces)! I know, that takes the fun out of it, but this is not the sort of project you want to do more than once.
Whether you use Xylene or Acetone to prep the tub, wear gloves and make sure you're in a WELL VENTILATED AREA! That stuff will kill ya!
Finally, wear throw-away clothes. Between the Herculiner and the Acetone, you'll never want to wear them again.
Good Luck!
Go easy! You're talkin' to a greenhorn.