I'm going to glue my fret board back on my neck but the nut is built into the fret board so I can't square it up against anything. What's the best plan of attack?

And as well I have a fair bit of wood missing on the fretboard on the 7th fret (just a screw around guitar nothing too fancy) what the best stuff to fill it with and how?
If the frets are out of the board, give it a sand and pack the dust into the damaged area then drop in some real thin super glue to bind it in. Leave for a day or 2 then sand back to level. Squaring is just a case of making measurements so that 12 is in the right place and properly perpendicular to the centre line.
You can use an Epoxy if you really want a hard area on the fret-board. Or you can do what is suggested above or you can use a good quaity wood filler.

You want to mesure the nut to the 12th fret, then double that number. set all the saddles on the bridge to the middle of their adjustments and make the nut that distance from the saddle.

When you glue the fretboard on, make sure the wood is sanded nicely. use enough glue to get good coverage, but be careful of excess because it can get on the truss rod and ruin the ability to adjust the neck releif. Clamp it really good. I use Franklin Tite-bond glue with no issues
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