Ok. Here's the ship I made to get to Eeloo, land, and return in one uninterrupted trip.
Here's part 1: This gets me up most of the way to an 80km orbit around Kerbin. The side rockets and main thruster are all firing. Once depleted halfway up, the side rockets (all four) are jettisoned.
Here's part 2: This section gets me the rest of the way up to 80km and has enough juice left to get me into a fairly circular orbit (78-82km). In the photo, it's basically the bottom half of the rocket.
Here's part 3: This transfers me to Eeloo and is supposed to get me into an orbit around Eeloo. However, I ran out of fuel in this stage and had to use my orbiter and lander. The stage that I wanted to get me to Eeloo and burn retrograde to get me into orbit is on the left side of the photo. The orbiter and lander are on the right.
Here are parts 4 and 5: This is the lander and orbiter docked together after jettisoning from part 3. The lander is on the left, orbiter on the right. The lander is capable of landing on Duna, Mun, Minmus, and Eeloo with plenty of fuel to get back into orbit. In one emergency, I was able to use it to get back from Mun and land on Kerbin on its own. I love my lander! The orbiter stays in orbit while the lander lands. Then, I transfer everyone back to the orbiter, transfer any remaining fuel, and return to Kerbin, and land. However, I had to use almost half the fuel from the Orbiter and Lander to get into an orbit around Eeloo, so I was coming in on fumes when I landed on Kerbin.
So, I'm thinking part 3 is where I need to add more fuel, and problem then part 1 to compensate, to make sure I can get in an orbit around Eeloo without using parts 4 and 5. But, as it stands, this is the best ship I've made so far! Any design tweaks or suggestions are welcome. Oh, and just ignore the engine firing on the last photo. Really, the orbiter's engine should be in use, but I forgot to disable the lander engine after docking, so it's just a messed up photo on my part.