How exactly does a ship traveling from point a to point b do so in the warp? Is it one long flight to the destination, several jumps to systems between destinations?

It's generally described as several jumps, though the length of the jump will depend on the warp conditions you're traveling through. It's not that the ships can't stay in the warp longer, but the navigational uncertainty value grows the longer and further you travel. (Though some people/stories/books/etc. have been known to indicate single long trans-sector jumps.)

This is why the waystations in the Maw are so valuable, they're known locations to drop out and check your bearings in a very hazardous section of space.

These navigational dropouts also tend to be in the outer sections of systems and only for a short while, couple hours to a day at most, so it has minimal effect on gameplay and tends to be hand waved as just part of the transit.