Power ratings are always relative to a certain level of distortion. And distortion will increase at higher output levels. An example would be 100 watts RMS @ 10% distortion just to illustrate the point.
What you want is minimal distortion (though in a TJ, you don't need to sweat it too much). There is no real need to match amp output to speaker power ratings. However, more clean amp power is generally a good thing. Just keep in mind that if you push an amp near it's limits, the high distortion levels can actually blow speakers, especially tweeters (high frequency drivers). So, there is really no such thing as too much clean amp power but too little can and does blow speakers.
An ideal setup with an amp is to have preamp outputs on your head unit. Hook the preamp outs to the amp inputs (usually rca jacks) and connect the amp outputs to your speakers. Many head units do not have preamp outputs. Many amps have speaker-level inputs. So if you head unit has no preamp outs and your amp has speaker-level inputs, an alternative hookup would be connecting the head unit speaker outs to your amp speaker-level inputs.