I have already installed Noobs to operate my Raspberry Pi3.I would like to run Raspbian Jessie Pixel.Do they run side by side or do i need a different sd card for both?
The main purpose of NOOBS is to install Raspbian PIXEL and/or other operating systems for you and let you select which operating system to start when you have more than one installed. So yes, you can have both.
I'm not sure what you picked when you first booted NOOBS and did the initial install of OSes, but my guess would be that it was Raspbian PIXEL and you're now looking at the separate (non-NOOBS) Raspbian PIXEL download. You don't need that at all; you already have it via NOOBS.
If you hold down shift (as prompted) during the boot, you can bring up the NOOBS rescue menu again and it will show you what OSes are currently installed on your card.