There isn't anything to do to get the best quality of the files, when you import them AE, doesn't compress or do anything, they keep their native resolution/dimensions.
Maintaining the quality of the files is depends on what you do in AE, if scale a layer a lot larger then it is, it will start to look bad. Another gotcha is interpreting the video footage incorrectly. Finally rendering to a high quality/lossless file will also keep your video looking it's sharpest.
I'll also add the Michael Szalapski stock answer, since it's appropriate here:
Since you're new to After Effects, I would highly suggest you start here:
Link The resources there will help you get a handle on some of the basics.
Johnny Cuevas, Editor
Thinkck.com
"I have not failed 700 times. I have succeeded in proving that those 700 ways will not work. When I have eliminated the ways that will not work, I will find the way that will work."
---THOMAS EDISON on inventing the light bulb.