You should align the neck by temporarily installing the high and low E tuners and running some ordinary string to the bridge. This will let you see that the neck is running true by checking the gap to the fretboard each side. This is also a good time to ensure the scale length is correct - I normally check to the High E as the rest will need adjustment further back for intonation.



Sometimes people use a bit of thin veneer to take up any unwanted gaps in the neck pocket, but I'd do the alignment first.