In Episode 19 of Fate Zero, Natalia is in the baggage compartment when the ghoul (bees) take over the cabin.
How does she manage to safely get into the cockpit?
AFAIK, there is no way to get directly into the cockpit without going through the cabin. Thus it would be next to impossible for her to get into the cockpit without being overwhelmed by the bees.
Does the Manga shed any light on this?
The plane that they were in is an Airbus A300-B2 which has a seal-tight cockpit door, it should have been able to keep the bees out but didn't, which could mean that it was open during the incident. It still doesn't explain how she managed to dodge the bees through the cabin, which she would have had to traverse in order to reach the cockpit. It's possible that, unlike real bees, these magic ghoul ones are slow and you can easily dodge them if you knew where they were. Or maybe, she's just got crazy skills.
The Manga doesn't shed any light on how she got through the cabin, though the original light novels may.
My speculation, but recall how in Episode 15, Tohsaka Tokiomi could conjure a shield that killed Matou Kariya's bugs upon contact. Since Natalia can also use magecraft (as seen from the magic circle she drew to kill Odd Vorak on the plane), she may have conjured a similar shield to force her way through the cabin.
To supplement Jon Li's answer, the light novels do not answer the question either. The relevant section is the interlude at the beginning of volume 4. In the novel, they show almost no details of the event. They describe briefly the assassination and afterwards the bees taking over the cabin, but there is basically no description of what Natalia does between killing Volsack and radioing Kiritsugu from the cockpit.
However, it did take quite a long time for her to get to the cockpit--over 2 hours, and it's implied that it was a difficult fight, so she may have battled her way through the cabin.
