How to get there

From the airport: 

Take a taxi. The yellow ones immediately outside are expensive - for cheap ones take the white city taxis. To find them, cross the street outside the baggage area exit, go left up a ramp. Go into that building ahead of you and through it to the street on the other side - that is the drop off area where you will find city taxis. Go all the way to the left to get to the taxi stand. If comfort is your priority, just find a driver to take you to the Hagnaya Port. P1500 will probably be the cheapest you can get. If you want to go on the cheap, then tell the driver to take you to the North Bus Terminal. 

From Cebu City:

Take a taxi or Jeepney to the North Bus Terminal. For Jeepneys, 4L,3Q from Ayala to SM, 10M from Colon straight to the NBT. 23D from SM to NBT. Check for the list. Most Jeepneys around Cebu City head to Colon or Carbon (which is walking distance from Colon), so just hop on any that say those names and grab 10M when you see it. Specifically, 10M passed by on Colon: the Metro, Guisono, and a landmark all know and love, McDonalds.

From North Bus Terminal (NBT): 

Take the next bus for Hagnaya Port. They leave about every 30 mins, on time usually in the morning hours. Aircon buses are random, good luck. Both the yellow (Ceres) and orange (Cebu Autobus) go to the port. You'll be harassed by guys trying to get you to go with their bus, just tell them you're going to Hagnaya Port and they'll direct you. They might seem pushy, but they know where you need to go and they don't expect a tip. The price should be about P60 for non-aircon, P110 for aircon - make sure to clarify what the price is before you get on and if you feel overcharged, don't try to haggle unless you know there is another bus to choose from. 

From Hagnaya Port:

Grab your bags when the bus/taxi stops, or one of the port's porters will grab it for you. If you can't just ignore them, or actually have a big bag or two, it is best to just let them take it and tip them P20 after they've taken it with you to the ferry. As for the ferry, schedules change so don't try to plan it - just go on the next one.  They're all slow now - Fast Craft, from what is posted on their booth, has either suspended all or some of it's operations - for certain the 1030 at least. Island Shipping has a boat at 1130 for certain, that's all eye can vouch for. Prices are as follows:

Island Shipping RoRos (has first class cabin with a/c) : P135 / P170 first class

Super Shuttle Ferry (no first class, but the breeze is nice) :  P135

 Transport time is about 75 mins. P10 port terminal fee. BBQ chicken outside the port is really tasty, but not cheap.

Arriving in Santa Fe Port:

 If you don't have a hotel, then it's possible to just walk along the beach or beach road and find one (or listen to the hasslers at the port and go with them). If you do and they don't provide a transport, just accept one of the dozens of offers you're bound to receive by pedicab or trike drivers to take you there. Most resorts are a 5 min pedicab ride away. Price should be P10-20 per person. If you want to save as much as possible on hotel and transportation, just walk outside the port, continue straight, take a left when it presents itself, and you should see several places for less than P500 per night (but these are not beach resorts, so you have to walk to the beach from them).