The attack scope where located in the conning tower as you stated. But attacks could be done from the control room as well where the sky/observation/nightscope where located. This scope had a bigger lens at the top and thus better light sensitivity with the downside being that is was easier to spot. It was also shorter so the boat had to be closer to the surface which increases the risk to accidentally break through the surface.
So if it isn't to dark you should use the attack scope which is harder for the enemy to spot.
Both scopes could tilt their view up and down, but perhaps the sky scope was better at this? Anyway it could be used for searching the surrounding area and the sky before surfacing.

In the conning tower the second person had access to engine telegraphs and rudder control so he could directly steer the boat as the capten sitting at the attack scope commanded. Also the target computer controls where in the conning tower and that probably means that there had to be a third man up there. When attacking from the controlroom I THINK you still had to have one man in the tower manning the computer but I'm not sure, perhaps they had a second computer station in the control room.

See [w1.510.telia.com] for some details about the attackscope.
And [www.heiszwolf.com] then click on plans for a drawing of a type VII

Leif...