Next, let's make some small parts. These things will be duplicated and placed all over the ship, so it's easier to just model one of each and then move them into position. The more copies of each one that you plan to make, the lower you should keep the polygon count:
Before duplicating, of course, we'll want to add our materials:
Here's where I ended up putting the RCS/OMS thrusters (on 1/2 the ship):
The thrusters can be any size (scale) that they need to be, but the handles ...