While working out the interior arrangement I've been giving more thought to how this can work out.
Keeping in mind that this vehicle has to withstand the pressures of subsurface depths it's even more important I think to have a double hull. Also I'm envisioning three compartments. The rearmost compartment is really just a double access hatch arrangement in the unfortunate instance of the outside hatch malfunctioning or being damaged whether in space or submerged. Mind you with the outer hatch compromised it wouldn't be advisable to rely on the inner hatch at any serious depths.
The middle compartment (actually the useable aft compartment) is a staging/holding area for equipment. When on the surface the upper part of the outer access hatch can be opened to allow for performing or deploying experiments....or maybe even sneaking in a bit of fishing? (-:
A third access hatch separates the staging compartment for the forward control compartment. This is where the flight crew and personnel are positioned during flight or subsurface maneuvering. There is room for a crew of four.
Just under the forward lighting panel at the bow is a small panel with a retractable phaser. This phaser can be used for a variety of purposes including stunning (for deterrence) of threat life forms that could be encountered. Under the hull there is an off-centre panel from which a variety of probes can be launched either in-flight or submerged. Some such subsurface probes could be used to probe into further depths that might lay beyond the aquashuttle's capability or to extend the range of the craft's surveying.