First off, welcome aboard knorstu.
Second, practice makes perfect. I know this sound cliché' but its the truth when working the small pieces. Walleye Wacker has the best solution as the hooks themselves act as a guide for getting the keepers aligned properly and once set in their track they will not move when the mold is closed. Andrew suggests using the small paint brush modified to help adjust them once they are set in but need a nudge to get just right, while a toothpick might be a good tool to use too. Don't use super glue unless you want to deal with a bigger headache.
Honestly once you develop a pattern or system of laying in the hooks and the wires and have worked it a while things will move along nicely. It just takes time and patience. Those little Diner Shiner heads with the wires will reward you well if you take time to develop a system and practice, practice, practice.