Wow. Wish I could help, but you aren't providing enough information. As I'm sure you've noticed by now, this video game is very complicated...
I'll try to help with the Nonnah. The difficult part about protecting the ship in the water is keeping the TIE bombers off it. They come flying by in pairs, dropping bombs on your friends that cause a lot of damage. When the first pair of bombers fly in, shoot them down and trace them back
to where they're coming from. There is a point where they fly into the simulation, and you can expedite the game by waiting there and shooting them all as they come in one after the other. Once they're done (doesn't take long), rocket back to the Nonnah to provide cover for the shuttle as it leaves. On its way out, from the starboard side come a column of TIE interceptors. They don't cause much damage, so if you were successful in keeping the bombers away earlier, you'll only have to shoot down a few of the fighters to make good the shuttle's escape.
As for your code problem, I don't know what the deal can be. Are you going down and hitting "enter code" after putting in the letters? When the code is successfully entered, R2-D2 will make an "Okay!" noise. Which codes are giving you problems specifically--it could also be that you just aren't noticing the changes (RADAR and ACE aren't obvious when turned on at first).
Hope this advice gets you moved on. May the Horse be with you (an old Jedi Cowboy saying
"The entire universe is simply the fractal chaos boundary between intersecting domains of high and low energy."
--Imladil the pink hairless monkey
"Where do cats think catfood comes from?"