I really don’t like to give recommendations, because there are too many unknowns when talking to a stranger over an internet forum, so I just say what I’ve done in the past, or what has worked for me. You can take the info, use it if you find it useful, or ignore it if not. I’m not a pro or an expert, I have built a couple dozen boards, all for myself, and I don’t tend to try to meet any special protocol for how somebody else would do it, etc, I just try to find what works for me.
That said, I generally would glass the bottom first, and wrap the rails. Then the first layer of the deck. Then the second layer of the deck. I would want at least 2 layers on the deck and rails, and one layer on the bottom, plus a tail patch on the bottom. Some people want 3 layers of glass on the rails, its not mandatory for me. But then I also sometimes do as Gene Cooper did on his award winning board, and use glass in the fill coat (hot coat), he calls it a reinforced hot coat, and the glass is sacrificial, you will hit weave for sure, but not to worry, thats what its there for. Anyway, thats another story.
To be honest, I haven’t done a whole lot of boards with colored bottom and rails, and clear deck, so I don’t recall exactly what I did last time I had that situation. Maybe when I inset the deck it was when I was doing a swirl on the deck only. But it worked out fine, so I know it can work. And you can see from the pics I dug up, when I did do a clear deck I had to add a line at the rail, so you know my transition wasn’t super clean.
Anyway, I hope you have fun with your board, don’t take it too seriously, its just a water toy, and hope you get lots of great waves with it.