A uke is a great way to get introduced to guitar making - it is hard to make a geometry mistake. Your uke is a true flat top - there is no dome in it. If things go right for your body in the mold, the side at the neck block will be a 90 degree angle with the top, and the body end of the neck will be a 90 degree angle with the fretboard plane.
Bolt on the neck without a fretboard, and when you lay a straightedge on the top of the neck it should lay on top of the body - nice straight line. This is NOT the same as a guitar. If this is not the case, then sand as others have said (I use 80 grit with packing tape on the back to make it slippery on the body and keep it from tearing). Then use the sandpaper on one side or the other to move the centerline left and right. The fretboard is flat, not radiused like a guitar, so don't worry too much about centerlines of the neck here when you lay on the straightedge.
Look at this picture and scroll right to see a sequence you might consider:
https://www.flickr.com/photos/ruby1638/26188084380/in/album-72157662606115293/Once the fretboard goes on (I always fret before I glue on the board), you make your bridge (without a saddle) thick enough that a straight edge laid on top of the frets just sits on top of the bridge. The saddle then goes in and gives you all of the "action" height. And there is so little stress on things that you don't have to worry about the neck pulling up over time.
There is no one-way to do anything on an instrument - example - when I make my guitar necks, I shape the back, rounded part of a neck except for final sanding before I install the fretboard because the piece lays flatter and more rigidly on my jig than it would with the radiused fretboard installed. I just leave a little extra material at the fretboard joint to take down to final shape once it is glued on - I find this easier and more logical, but others won't. You will probably try a different method for a lot of steps on the next instrument you make (and there WILL be another instrument). I find if I take a lot of pictures, then I can better remember what I did last time
My daughter is right now running a ukulele camp for girls 10-15 years old in Brooklyn, NY. I was up there on Wednesday to help with neck sets on 10 ukes. She and I got a system down and had them all done in about an hour - these are Stew Mac kits, so most of the work is done already.
Good luck and ask questions
Ed