As you say, your Thomas Cook rep. will meet you at the airport and direct you to your tranfer bus/van. I would imagine that they will also let you know when your return pick up time is as well - or they may contact you at your hotel a few days before the end of your holiday to confirm the time.
I'm sure your rep. will answer all your questions and give you a local contact number so they can be contacted.
We have always organised our own transfers with a local Towncar company, but that is how I would expect things to work
The biggest downside of using the included transfers is that your transport will probably be dropping folks off at a number of hotels and resorts, so although it may be nice to see the other hotels, it may take a while to reach your hotel unless your lucky enough to be dropped off first

This also may mean that you are picked up quite early for your return trip in order to get have enough time to pick up at the other hotels and get to the airport in plenty of time.
If you fancy organising your own transfers check out the following for information:
FL Tours
Tiffant Towncar
It is a more relaxed way to start your holiday. Your personal Towncar driver meets you in baggage reclaim, helps you with your cases and then takes you direct to your hotel (via a grocery store if required to stock up on those vital in-room snacks).
I know it's an added expence when your already have a 'free' transfer, but well worth it in my opinion

You could also really splash out and have a limo transfer
