Aligning the mirrors is called "collimating" them. It sounds as if your scope is of the Newtonian variety--a main mirror at the bottom, and a diagonal mirror reflecting the image to the focuser/eyepiece.
Try this: go to google.com and enter the following words into the search engine:
collimate Newtonian telescope help .
You should then receive a list of several articles available on the web answering your question in detail. Enjoy.