If anyone ever gets in the same situation - it worked as I wanted.
I didn’t put in any FF ID in the booking.
Qatar allows at each online-checkin to name/override the program where the flight shall be credited to. (Also applies to connecting flights, doesn’t look like one can split these, but I didn’t need it)
So left blank for 1st leg. And all others added my VA ID. I just waited until the flights have regularly been posted to my VA account (was really slow this time) and then put in a points claim for the 1st leg at QF.