How do you count your private/total study time?

The later.

Do you count the time you studied from the time you start in the day until the time you stop working or alternatively do you count your private study time in terms of the time actually sat down at your desk?

I count from when I sat down to when I finished. I exclude breaks longer than 10 mins though.

If I go to make tea or have a smoke, I'm still thinking of ideas, course of action or going through what I read in my head.

That's fair enough! It's just that some people say they've done 8 hours because they started work at 9am or something and finish at 5pm for the day. We all know though that one cannot work for long sustained periods of time without a break, so even if people sit down for ages, the quality of that time is diminished significantly. And if they take large breaks ie 30 minutes to an hour that surely cannot count as time spent "working".

I count my study in terms of content rather than time! So I'll have goals for stuff I want to do that day, and try to do it in the time I've got available. If I finish it all in an hour - great! Day off! If not, then it's a long day!

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That's quite a good way to go about things, but do you not feel guilty even if you have finished your work that you may perhaps be wasting time? I mean you could potentially re-visit other sub-topics or do further reading if you're at university?! Just a thought..

That's just part of taking responsibility for your own learning. "Revision" and "Wider Reading" come under the goals, as well as primary curriculum study! Part of the responsibility of university study is good goal-setting: knowing what you need to get done, and when you need it done by! Never feel guilty on those "off-days": sure I could do more revision, or more further reading but a good work-life balance is just as important as study: I'd grow to hate my degree and my time at uni if I didn't get the balance right!