I think everything on the planets counts towards you as soon as you land, including any missions there.
I have to stress that I'm not 100% sure on this, though. ME2's morality system is weird.
In any case, once you start the loyalty missions, do Miranda's first, then Jack's. Make sure you have a save before Jack's since hers is a bit shorter if you end up needing to try the respec trick.
Or you could just respec ahead of time, but that does waste some credits.
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Gamertag/PSN-Murphiroth
"Would have liked to run tests on the seashells..."