I can't remember how many had cells like that, honestly after I saw them moving around I got so worried I wasn't really paying much attention but I think only 3 or 4 out of 12 were like thatNow we're in a "She said, She said" situation. Truly, either way will probably work, and most important will be to watch your air cell size. If the chick grows, it should push the air cell to the right position, especially if you lock down with the fat end up.
Go with your gut instinct.
Ravyn has much more practical experience than I do, I've just been doing a ton of research since most of the time, shipped eggs are my only option. The latest info (Thanks to Ruby) made a lot of sense on how inadequate turning during early incubation can cause more deaths later (near lockdown). Manage your incubation to support your best eggs, don't risk the "good eggs" to try and save those that may be too damaged to survive anyways.
I can only tell you what I will try next time I receive shipped eggs. Good luck!