When the German U-boat leaves for the island in the ocean we see Indiana Jones on the outside of the deck. Any information if the U-boat traveled on the surface the entire way? If it submerged I would think he would have floated off or some how he managed to get into the u-boat unseen. Any answers out there?
The script reveals that Indy attaches himself to the periscope:
Indy climbs the ladder to the top of the turret and braces himself between the two uprights there--the 7 foot radio mast and the 20 foot periscope.
Still the ocean comes up to meet him. Soon the top of the turret is under water and the radio mast is disappearing.
Indy shifts his grip to the periscope, working his way up it and hanging on for dear life as the ocean whips at his body. The periscope is quickly going under. Indy hangs on to the top three feet, all that remains above.
The forward movement of the sub continues, but, to Indy's slowly dawning delight, the dive stops. No more of the periscope goes under. Indy smiles; it's a pretty good smile, too, given the circumstances. Indy pulls out his bullwhip and begins tying himself to the periscope.
And it seems that at least some of this was filmed:
The periscope ride
This is the most well-known of the Indy cut scenes, by virtue of being the one most crucial to the plot. This scene explains how Indy survived his trip at sea attached to a submerged submarine. As the sub descends, he climbs up and grabs hold of its extended periscope. He then lashes himself to it with his whip for the long trip.
This cut scene did make it into the Marvel Comics adaption: