Help with Online Check-In needed
 

I'll be using the QR OLCI for the first time. Their OLCI opens 36 hours prior to departure, and since I'm flying two legs () this was a bit confusing.
I OLCI'd precisely 36hours before my journey begins, but this was 43 hours or so before my second leg. Is this normal? Should I then check in again later (but using DOH, my stopver point as a point of origin)?
I'm really cautious about this because I know from experience (on other systems) that messing up the OLCI function can result in Weird Happenings (e.g. I was once told 'there is no record of your booking sir'...etc).
Thanks in advance