Should I put the SSD in the Optical or Main Bay when replacing Optical Drive?
You should go ahead and do what you first propose of the SSD in the optical and the HDD in the main.

There are two things to consider with speed, data rate and latency.  Data rate is how fast the data can transfer from point A to point B.  Something to keep in mind though is HDD are not that fast and may not use the full 3 Gigabits it is given.  A WD green drive is made to save power and reduce heat.  This means it spins slower, so it can't pick up the data as fast.  As a result you are not at transfer link saturation.

The SSD does not need to spin and and only access one part of a file at a time, it has the entire drive accessible.  As a result it can saturate the line.

Latency is also important, it takes time for the HDD to get to the files that are needed, for the SSD the files are already there.  As a result, during boot the computer is not waiting for the next file to come around.  It can go file after file after file.  Reduced latency means faster speeds.

Already your first proposed setup is wining, but while doing some research, I found answered question: What is an SSD drive&#39;s negotiated link speed?.  The optical bay is capable of 3 gigabits per second, however, the negotiated speed is 1.5 because the optical drive is slow and doesn't need the 3.

The optical drive negotiated for a lower speed but can handle faster on the bus. If you already have the drive one thing you can do just test it out yourself, try one configuration then another. There is a free program called Black Magic disk speed test (itunes.apple.com/us/app/blackmagic-disk-speed-test/id425264550) that measures your hard drive speed.