We went over some aspects of Illustrator today to prepare for next weeks project at RIT. There are just a few things to remember.
After you work out a tight sketch, scan in your line art at 300dpi.

Open up the file in Illustrator. To keep from saving over your original scan, go to FILE> SAVE AS and save the document with a .ai tag (ex. finch.psd saves as finch.ai). When I work this way, I delete the photo every time I save to keep the file size down, then just EDIT>UNDO
(command Z) to bring it back after the save. This is an old habit from illustrator 7 and 8 where the files would often become corrupt if it had a .psd in it. At least mine did.
I drew this on tracing paper, starting with a very rough sketch to work out composition and patterning. I took that and traced over it refining the forms and then a third time for better clarity. Think of Illustrator the same way. Its just another stage of refinement.

Add another layer over the scan. Create a large square or rectangle and fill it with white. Set this on a TRANSPARENCY (pallet found in WINDOW) that you are comfortable with so that enough of the art shows but not so much that it competes with your path color. I chose 90%. I left some edges peak out so you can see the contrast.
Add another layer for the paths. You are adding layers so that you can turn them off and on. You will want to turn off the sketch to see the development of your paths. I always lock these layers so I don't select them by mistake and that they don't get in the way.

Now that your set up, your ready to start the paths. The path tool (Pen Tool) has 4 functions. The tool itself that creates the path, the add points function, the delete points function, and the convert points function. When the tool is selected, it will add points on the path if you just hover over the section you want to add to and click on it. The same goes for subtract. If you click on any existing point, it will delete. The particular path must be selected at the time. To change the direction of the handlebar, use the convert points function to select one handlebar and bend it.

Click and drag if you want a curve. Look at the handlebars. If you want clean, equal curves, both sides should do equal work and so the handlebars should be the same lengths (see the light blue lines above). If there is an unusual bend, one handlebar will be longer, pushing the path into the other point. The fewer the points, the smoother the curve.
The above lines were duplicated and moved to ensure the line is parallel (EDIT>COPY>PASTE IN FRONT and nudge one point with the arrow key). The blue line, now a shape, is joined at one end. You will need to join the two ends to make a workable shape. Do this by holding down SHIFT, select the end point on each path >OBJECT>PATH>JOIN (command J).

Once you have your paths made, you can start cleaning up the shapes. In the finch image above, you can see that the dark blue shape is longer than it needs to be. To get rid of this extra end, I would:
1. COPY the orange shape (after joining the ends)
2. PASTE IN FRONT of the blue shape.
3. holding down SHIFT, select both the orange and the blue,
4. in the PATHFINDER (found in WINDOW) subtract from shape area. That's the second button in from the left. Remember that the shape on top will be the deleting shape. That's why you COPY it. Because it will delete and you still need it.
5. Click EXPAND in the PATHFINDER pallet.
Play around with the PATHFINDER pallet. Concern yourself mostly with the top row for now. The first one combines, the second subtracts from shape, the third intersects, the forth excludes.
When you have cleaned up all your paths, combine them together. Now you can select the parts individually to fill with color. Using the hollow arrow plus, select the piece you want to color, COPY, PAST IN BACK and chose your color. You need to use the hollow arrow plus because you are selecting part of a GROUP.
It may seem awkward at first but this whole explanation is done in minuets and repeated and repeated until done. You will fall into an enjoyable rhythm. At least I think its enjoyable.