| Slip-ons are for better sound and aren't really a big performance enhancement. At the most, you'll get a 2-4 peak horsepower increase (@ 6,000 - 9,000 rpm respectively for Termignoni's.) EPROM chip makers usually are just bringing the mixture back from the slightly lean condition that Ducati uses to meet emission targets.
Generally you can put the exhaust cans on and have your dealer re-adjust the CO level to compensate for (minor, if any) increased airflow. There's a CO trimmer screw adjustment on the ECU that provides for limited fuel mix increases. The trimmer affects fuel delivery over the entire rpm range, but with a lesser effect at higher rpm. Go easy, a half-turn on the screw is all that's usually needed and too much fuel affects throttle response and idle adversely.
Always a good measure is check the color of the inside of the tailpipe after a few hundred miles. It should be light to medium grey. I can't tell you how many chipped Ducati's I've seen running around with blackened pipes just pouring gas money out the back. BTW, half or full exhaust systems DO need revised EPROM's since they do significantly increase airflow and do require increased fuel to compensate and prevent severe lean conditions that damage engines.
That said, I bought a Ducati Performance chip having a generic slip-on fuel map. The improvement in low end throttle response and horsepower at the top end is noticeable. The tailpipe color is medium grey now and the gas mileage is down roughly 10 - 15%. The rev limiter rpm is also raised. However, the mixture difference between cylinders is now more noticeable. One tailpipe is less grey indicating a leaner mixture. This bears out the major selling point for FIM chips is that they have different fuel map adjustments for each cylinder, the other brands do not. But, in order to take full advantage of FIM chips you need to make some dyno runs with an experienced tuner.
However, dyno tuning usually involves setting the fuel mixture for maximum horsepower at high rpm. Best power is usually realized when full-throttle CO is in the 4-6% range. But be careful, this may also result in an overly rich mixture at midrange rpm where you do most of your riding. Your choice.
Finally, all EPROM chips sold for aftermarket exhausts are not the same. They usually provide enrichment (over the stock chip) across the RPM range but some bikes just - don't - like certain chips; Ferracci chips, for example, tend to be mentioned most often regarding overly-rich mixtures causing stumbling in the lower rpm range.  | 
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