Our experiences with ferries have mainly been with the continental operators DFDS, Stenaline and we have also used some of the ferries that link between Denmark, Sweden and Norway, and have found that they are all very similar in the way they work.
When you book your ferry you must state that you have a cycle, even if there is no charge for cycles as the cycles may need a boarding card. I know this may seem funny but at Esbjerg we got slightly delayed because our tickets only showed one cycle and we had two, it was easily sorted at the main terminal check-in desk but it was a bit of a pain.
The cycles board with the vehicles generally, so you must report to the vehicle check-ins (the only exception to this seems to be at Fishguard where you board through the passenger check-in and are then escorted by a circuitous route to the vehicle ramp). You are then directed by the ship's crew to the areas of the car deck where there are usually ropes to lash your bikes to railings or to the deck sides. It is worth spending a bit of time making a good job of this, as if it is a rough crossing you don't want your bike moving about.
As far as being secure, the first time we used a ferry we removed all our panniers and took them to our cabin, but it was a right hassle and really there is no need as the car decks are closed 15 mins after departure and only re-opened 15mins before arrival. (We now only take with us our bar bags which contain our valuables and a front pannier which contains clothes and a wash kit). We have had no problems with security or damage, but remember that most ferry companies have a limited liability for damage (check the details on your ticket) so you may wish to make sure that your bike and luggage are insured as part of your holiday or house contents insurance before you leave for your trip.
As far as charges for bicycles are concerned it very much depends on the company and the destination. You will need to check with the ferry companies when you book.
We have also used the Caledonian MacBrayne (CalMac) ferries that operate the Hebridean and Clyde ferries in Scotland. As a cyclist you don't generally need to book the ferries as you can just turn up at the ferry terminal. For the smaller ferries you can purchase the tickets on-board but with the larger ferries you will need to purchase them at the terminal building. Caledonian MacBrayne do a series of island hopping 'Hopscotch' tickets that are valid for one month and may work out cheaper than buying the individual ferry tickets for your tour. Caledonian MacBrayne produce a useful free Android smartphone app which gives you update information on sailing times and the potential cancellation of services due to bad weather.
Ferry Company Links
† (We are told that the P&O ferry to Ireland unfortunately does not carry bikes).