Some replace the Hard drive with the SSD and some replace the Optical drive with SSD.
I would recommend putting the SSD where your original HDD is.
I found a link which may be interesting.Upgrading Your MacBook Pro with a Solid State Drive
I checked my computer information under "About this Mac" and it shows the Link Speed and Negotiated Link speed of 6 Gigabit for my SSD in the place of the original Hard Drive.
The Hard Drive which I have put into he Optical bay shows the Link Speed and Negotiated Link speed of 3 Gigabit. But I have not noticed it running slow. I use it for storing movies, music, etc.
If you are planing to upgrade to El Capitan you can upgrade before or after upgrade.
By using Carbon Copy Cloner (CCC) you can clone your existing Hard drive using an external USB case or the cable I used.
http://www.amazon.ca/gp/product/B006J2L0ZM?psc=1&redirect=true&ref_=oh_aui_detai lpage_o07_s00
If you using CCC you can actually boot to the SSD while in the external case and test it, once you have cloned it. Once you are satisfied that it is working ok, you can replace the Hard drive with the Cloned SSD. Keep the Hd on you desk for a while and if everything is working ok, you can either put the old Hard Drive in an external case or you can put it in place of the optical drive. (Most find the Optical Drive of little use these days.). If some unexpected emergency happens, you will still have your original hard drive to put back in.
Check the OWC site for information and videos on how to do it. http://eshop.macsales.com/installvideos/macbookpro_13_unibody_early11/
Kim