Ok, everyone needs to take a step back and forget anything you have heard or read about or pictures you have seen regarding Torpedo loading before 1970..
To answer the first question, yes, port and stbd. Not enough room to do both upper and lower tubes efficiently together.
See pic..
This is a fourth flight 688 (688i) and the two tubs on the left are tubes two and four. You can see that it is faster to do one each on each side simultaneously.
All torpedo tube loading is 'powered'. The boats do have a block and tackle for this purpose but it is the 'emergency handling gear'. If you loose hydraulics then you use this... If you have lost hydraulics, then you are in a WORLD of hurt...
Once you get the weapon into position in front of the tube, then you pivot the tray to align it with the tube (cant). Attach the loading pole to the aft end of the weapon, the pop all for straps that hold the weapon to the dollies. Then set the pivot tray to the depth own ship is currently at.. (important).
Then start ramming the weapon into the tube.... slowly.. After the weapon is fully loaded, the lock the weapon into the tube. Remove loading pole, and finish the loading process... cables/wires etc.. which I will not go into here.
In the first picture that was posted yes, you have to remove the upper level and middle level decks. That is one of the reasons I stated that it takes two or three hours of setup before you can ship the first weapon. Usually it takes all day.....