It's been a bit since I used it, but I recall an overlay that does the hexes for you. I'm not sure what you mean by line up. Line up with what? I recall being able to change the hex color and even offset it a bit.
The overlay is by default not visible with printing, only for designing. But, there is an option to make it visible and alter it's size and appearance (squares, hexes, size, color, etc).
With the grid made for you, I would make a template of world symbols, starport letters, naval symbols, etc. These could even be grouped so you could drag and drop copies to the appropriate hex. The most laborious problem would be typing in the hex numbers and placing them (if you required this).