Read Panama Formalities for detailed information on procedures for clearing into and out of Panama.
There is Immigration in the port as well as the Port Authority (Autoridad Maritima), where you can do all the other paperwork and get the cruising permit or a national or international zarpe.
If the Immigration office is closed, just wait for the next day or go to the "Migration" office in Santiago to get your passports stamped. Just take the bus (1.30$) and then a taxi to "Migration" (1$).
It is reported to be very straightforward and only minimal fees are charged.
Last updated July 2012.
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