IMHO the best transport option would be via a rental car.
As to a touring plan - on "normal days" (no scheduled shuttle launch) your regular admission ticket entitles you to 2 day's admission (consecutive days).
Personally, if you've never been, I'd recommend spending the first day touring all that's offered at the Visitor's Center. Making sure to catch at least 11 IMAX movie, One of the Mission Status Briefings, and the exhibits (I particular like the early exploration exhibit) as well as doing the Shuttle Launch Experience.
On the 2nd day I would do the bus tour and then with any extra time, go back to the visitor's center to check out anything you missed or wish to re-experience.
As to Launch days...it's abit different.
Admissions on launch days are special ticketed events. This is because the visitor's center is set up with a huge TV and live audio feed from the Pad. If you want to get even closer (about 6 miles) from the pad you'll need to purchase a transport ticket (these go EXTREMELY FAST!).
If your planning on visiting near or on a scheduled launch day I'd strongly recommend you visit
http://www.kennedyspacecenter.com/special-programs-launches.aspx for launch specific information.
I hope you visit and enjoy yourselves!
HTH