Your passports don't have anything to do with seat reservation. 

You only need the passport numbers to activate the passes right before actually travelling. This last step is usually done on the first day of travel. Once the validity period starts, it cannot be undone.

Getting seat reservations doesn't require passport numbers and can be done on multiple websites, if available through the railway company directly to save on fees. Have a look at https://www.seat61.com/interrail-and-eurail-reservations.htm

https://www.seat61.com/how-to-use-a-eurail-pass.htm

The only exception would be the Eurostar from/to London. On Rail Europe they do ask for passport numbers (API form required by the British government).

For more advice, let us know the route/travel date and we'll gladly help.

I have tried to book the seats from Como to Naples and before I can check out, it requires me to enter the passport information. 

If "it” is the Eurail website, then book somewhere else. That will also be cheaper. Eurail have an extra booking fee of €2 per person and train. The best place to book is www.raileurope.com. No passport number needed.

For Como to Milan it's best to use a regional train, so you save €10. Milan-Napels is €13 with a fast train.