The most important thing is to proceed directly to check-in and do not attempt to anchor or dock anywhere else, no matter what time of day or night you arrive. People have been arrested and fined anchoring elsewhere after arriving late at night. You won't be able to check in until morning anyway, but at least you are in the check-in port.
The port authority office is located next to the bar on the NE corner of the town dock and this should be your first stop.
I docked on this eastern dock and was allowed to stay there just for the check-in.
This is where you get your vignette documents and pay for the cruising permit. Check in is very friendly and easy. It cost me 1085 kunas (€150) for 10 meters. This is valid for 1 year.
I attached the vignette sticker to the starboard side of my mast, just above the deck, but I was warned that they don't come off very easily and could damage your paint.
You are also given a "LIST OF PERSONS", which is intended to limit unauthorised chartering in Croatia. You are meant to fill in every guest that sails with you during your stay in Croatia (not including guests at the dock). The number of possible guests is calculated by your boat size and the number of berths. When the list is full: no more guests.
After clearing the port authority you need to walk around to the opposite side of the port to the small customs and immigration portable building. They are not always there and you may need to call +385 208 01021.
Customs simply asks if you have anything to declare, and immigration stamps your passport. You, personally, are allowed 90 days in Croatia. The boat's vignette is valid for one year.Howard [ Just Imagine ] 14-Jun-2007
Customs and Immigration (Formalities)
Port Authority (Formalities)