I am currently half way through making my own guitar but have come to a stand still point because of my fretboard. I have a 12" radius fretboard with binding around the edge and I didnt know of any other way to get the frets to stay down on the binding except by gluing them.. This is where my question comes in, am I doing it right by gluing the frets down on the binding because it is very messy and I feel like I'm doing it wrong because I have to scrape excess glue off the the fingerboard. I dont want glue residue to be left over on the fingerboard when I'm done but I cant think of a different way to do it, but this is my first fretboard so any tips would be very helpful.
Is it wrong to be strong.... You decide.
I will try to explain what i think should happen.

Make the fretwire as long as you need (to go from one side of the neck to the other, making it long enough to lay on top of the binding like you want).

You prebend them to the correct radius, and you PRESS them in. In order to make a spot in the binding for the frets to drop in, try cutting the fretwire. Dont mod the binding at all.

So the fretwire piece will have wire, but on approx 1/16" on the both ends, it wont have those teeth that usually hold it into the fretboard. I dont know how luthiers do it, this is only a guess.

My other would be to cut with a special knife or saw the spot for the fret to press into the binding. I know the slot for the fretwire on a bound neck doesnt show, so this might be tricky seeing as you already have it on.

There are a bunch of people that know more than i do, you should ask other guys (like ormsby, that dude is retarded......ly awesome)
What he suggested about the teeth is what I've always thought was done for binding necks... but like he said, I don't know for true either. I can go ask my roomy (he's an apprentice for a great luthier) and he would definately know.
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I cut off the teeth/wire part to lay over the binding, but I felt like it could be grabbed and pulled off by the string if accidently overbended or something like that so I tried gluing it. I can post a picture of what I have done already when I get home in like 20 minutes. So far the gluing part is securing the frets to the binding just fine but I was mainly wondering if i was doing it the correct way because the excess glue is very messy and I have to scrape it off the fingerboard after it dries.
Is it wrong to be strong.... You decide.
Under cutting the fret wire is the way its done with bound necks. There is special tool to do it but I use a dremel and alot of patience. And of course putting the bevel on the end of the fret wire and dressing the ends is a whole lot of to do without tearing up the binding. Im sure the pros can do it pretty easy but Ive only done my epi. I know gibson sells a precut pack of fret wire. Maybe it would help. I just know bound fret boards are a pain in the butt. And I like stainless fret wire which is even harder to work with. I know warmoth wont do stainless on bound fret boards. And you can use glue or epoxy. I use it sometimes. I use a toothpick to put a little on each side of the tang then press them in. And wipe the extra real quick. Ive seen where some put wax on the fret board so the epoxy wont stick.
As this is your first fret board I will warn you there is a steep learning curve. You are much better to practice on some less valuable necks before you tackle your project guitar. My first fret board was pretty bad. And you will need to spend some money on proper tools, you wont be able to get them at a local hardware store. Stew mac is where I get all mine. Good luck. You can send messages to me if you need any pointers.