I know can explain it beter than that! Of course they can stay submerged and travel with the MBT's flooded. That is the normal operational mode. They would still have their trim system working for ballast control and, as you mentioned, the planes.
Going to the surface just requires adjusting the planes and up you go. Now to "ride on the surface" you need to blow the ballast tanks. Photos show that they had a "continuous" blow on a forward ballast tank. (I put all this in for the others, not for your sake).
"I know can explain it beter than that! " >>>I know can YOU explain it betTer than that!