Normally you will get 2-3 days in the San Blas Islands depending how much time the captain has to allocate to the crossing.
No, to the captain you have to pay in cash and preferably in US-dollar. The captain can accept Colombian Pesos in Colombia at an exchange rate set by the captain. Please contact your captain directly to get his rate. You should have his e-mail in the confirmation of booking received when you made the deposit payment.
Cash payment in EURO is not possible, but some of the captains accept EURO transfer of the final payment to their European Bank account, if they have one. Please contact your captain for more info about this.