Illustrator has many color systems in which to pick colors from. In Illustrator 10 & 9, you go to Window->Swatch Library, from there you can choose form various swatch librarys. I can rember where in previous versions but it is similar. The palletes (> ) sub menu will allow you to change the view as to see the swatchs larger or with visiable lables.
In illustrator you have the (Document Swatchs) and (Library Swatchs). If you create an object and select a pantone color fom the Library swatchs it will be placed into you document swatchs. From there you can adjuct how the Pantone color will be treated apon output. One can also drag a swatch from the library swatchs to the document swatchs and then use it from there.
You may need to decide on how you are going to treat your Pantone colors.
A. If you are just doing web or printing on an inkjet/etc... printer you should not have to make any changes to the swatch in the document swatchs. They should be useable just the way they are.
B. If you are going to press and planning to print the pantone colors as a Spot colors, (IE. printing ink for each color in the illustration.) Then the default setting should be ok, and pantone colors in Illustrator default as spot colors.
C. The tricky bit is If you want to try to simulate the pantone color using 4C process inks on a press you will need to double click on each of the spot color and change the color type to process, and the color mode to CYMK. (Changing color mode in not realy necessary but it works as a double check to review the number generated as not all Pantone inks are reproduceable in 4-Color.)
jstuartj