Go on the flexi clock immediately. It is proof that you are there. Sick leave regulations say that you can take 7 days in 5 occurances per year uncertified, but Revenue are strict if you go over this. If there are genuine reasons for being sick, this is usually accepted, though the pobabtion period may be extended for a further year.
And most people take the flexi day off every month, assuming they have built it up, and it is not frowned upon by any means when you take it. As for 'watching the flexi', you get an infringement if you arrive in late, leave early, leave early for lunch for or arrive back late from lunch. If there is a genuine reason, your supervisor will discount the infringement, for example if the flexi clock is not working or you are out of the office on business.
Good luck with your career, and definitely go on the flexi as soon as you get a chance. And there are no plans to phase it out in the civil service
As to what the job will be like, it very much depends what section you will be assigned to.