Since there have been lots of threads on this subject but not a lot of answers I thought I would share my experience of the new check-in system.
My flight is from Prestwick to Faro on 14.05.14 returning on 21.05.14. The first thing is that you can login to your flight and put your API details in up to 30 days in advance whether or not you intend to check-in. This saves time when you check-in later.
I decided to take a chance on the 7 day free allocated seats. You login to your flight and you are faced with two options, Purchase an allocated seat or free randomly allocated seat. If you chose the second option then it will tell you the date you can check-in. In my case this was 7.05.14. There is a lot of debate about when in the day you can do this so I tried on the 7th at just after midnight even though my flight is at 16:40 it allowed me to check-in. This is great because if you are on a 7 day holiday you can check-in your return flight on the day you leave, saving you paying for a return seat or printing a boarding pass when you are away.
Before I had tried the free option I clicked on the purchase option to see what seats had already been taken. Only 16 out of the 198 seats had been allocated so their take-up of the charges is poor. I did this to see if there was availability of seats together. I should also point out that the seats would cost me £10 each for this flight and £15 for the premium ones.
So I came back out of this option and chose the free seats. You do not get any choice and neither do you know which seats you get until you have completed the process and view / print your boarding cards. We got seats 18D and 18E which are together and I believe the row behind the premium exit seats. This disproves that Satan's Airline would deliberately put one person in the hold and the other outside on the wing if you don't pay up.
Sorry if this is long winded but these are the answers to questions that may help others decide whether to pay or not.
My summary is that if you want to take a chance on the free allocated seats, check-in as early as you can to try and get seated together, but IF it is important for your family or group to get seated together then bite the bullet and pay the price. It also suggests that they fill the plane from the middle first.