Whatever you do, don't buy the book "How to build a Pole Barn" by Mathew Logan. Worse written book I've come across. Confusing, missleading and impossible to follow. Just read the posts from Mopower.
If you're financing this through your bank, then they will decide what you can and can't do. Each banker has a different level of trust in how you spend their money.
If you're paying out of pocket, then I'd recomend staying single story. You have the land, so space isn't an issue. The second story is much more expensive per square foot to build and requires more skill and engineering.
Consider your demensions to reflect available lumber sizes. Can you build your own trusses? How far of a span do your really need? I went 24 feet because it was an easy span to build for with off the shelf lumber. If you go 40 feet, then you're going to have to spend a premium on engineered trusses or glu-lam beams.
You don't need concrete in the barn, but the apartment needs a floor. Wood is too expensive to for pier and beam. So you must consider if you can poor a concrete slab. If not, figure $3 a foot, maybe more for a small job.
I'm a big believer in planing down to the smallest detail. I use a program by Broaderbund called 3D Home Design Suite Professional 5. Pretty easy to figure out. The real advantage is you can draw your walls, add furniture and get a real idea of how much space you need. You will also figure out where to put the toilet, shower, sink and vents.
Hanging sheet rock isn't very complicated, just a little physical. You can rent a lift for around $40 a day to do the ceilings and the walls are a simple one man operation.
If you take your time, plan everything out, do the research, there's nothing you can't do by yourself or with a few friends.
Every contractor you bring in is going to charge you for matrials, which might not be the cheapest available, but the most convienent for them to get, and of course they will need to make a profit for their time.
Good luck,
Eddie