I think a lot depended on the circumstances.

Conventional ships are refuelled by bunker barges and I would have expected this to apply to u-boats as well. In the early part of the war and where u-boat pens were not available I am sure this would be how it was done.

However... In more remote areas it may be more "agricultural". There is a picture appearing in many books which shows I think a type IX with many oil drums on her after deck.

In the u-bunkers I suspect it was done from a manifold and undeground pipes built into the pens. With the RAF getting more aggressive it would be sheer folly to fuel these boats outside.