Short answer - It doesn't matter.
Long answer - If you have a balcony and sit in your room watching the transit you will miss a great deal of the adventure. There is no way to get a feel for the transit from any one perspective. Watching as the ship enters the locks from a frontal perspective is great and is what accounts for the crush of passengers at the front of the boat. A lot of passengers miss the opportunity of watching the entrance or exit or rise while in the locks from the back of the ship. This offers a truly fascinating perspective.
The transit takes the full day. At times there is a lot to see and much activity (entry and filling of the locks). At other times the locale is notable without much activity (passage through the Galliard Cut). And some of the time there is nothing much going on (crossing Gatun Lake).
There are six locks for the transit and you never know which of the sets of locks your ship will be assigned. My advice is - don't worry about a specific side of the ship. Before the cruise using diagrams and at the beginning of the cruise by actually exploring search out the observation areas of the ship. There are the obvious areas which will be most heavily used. There are numerous other areas that are slightly more difficult to locate. These will not be as well used and they will provide you with a wonderful vantage point for the transit. During the transit move around the ship - front to back, side to side using the areas you have predefined.
We cruised the opposite direction that you going but you may find my review of the cruise helpful. It can be found at http://www.cruisereviews.com/princess/Sea12.htm
I would be happy to answer any questions you may have. You can send me an e-mail at email@example.com
[This message was edited by Blackrobe on May 28, 2003 at 07:52 AM.]