I know with my games that I use all of my reasearch points for the background tech, and use the instant sm function to get the actual designs that are used. Unless you are starting with a really huge (5billion) population you will need to do it that way or you will not have the points to do much reasearch. This is also how the computer does it when you let it design your starting ships. Try it out and see what you get. If you let the computer design your initial ships, I usually reduce the starting total by 10% and keep track of those points on paper. This lets me fill in major holes in the reasearch that the computer auto-generated. I have had such wierd things as extremly good turret tracking speeds, and no beam weapons that could be put in them, stuff like that can often be filled in with fairly low point cost reasearch before you actually start the game.
Hope this helps you
Brian