All of the modern anti-malaria drugs are pretty serious medications, and have side effects that can be detrimental to your over all health
. Many of them can only be taken for a limited period of time, and as atoll says, some are not effective against all strains of malaria.
Considering these factors, we've used the philosophy that avoidance is better than medication. That is, we employ physical barriers (screens, isolation, clothing
nets if required, etc) rather than prophylactic drugs. We do carry Malarone dosages to be taken if required, ie at the onset of suspicious symptoms if blood testing is not available in a timely fashion.
We have not transited the canal
nor visited the San Blas, so I will not venture an opinion on the likelihood of infection there, but our methodology has seen us through long stays in Malarial cruising grounds elsewhere.