I wrote up an answer and then looked up the Lenovo Yoga 3 Pro and see it is the most modern design using an M2-2280 storage type. I discarded my old answer. Here is a corrected one:
http://download.lenovo.com/...70_hmm.pdf
Whatever you see for answers is wrong unless they start at that point.
"If I order a second 500 GB drive and physically install the drive"
The only drives that fit inside the laptop is a M2-2280 type.
480 to 512GB
http://pcpartpicker.com/parts/internal-hard-drive/#t=0&xcx=0&f=122080&sort=a10&page=1&S=400000,8000000
Normally, if there were a standard 2.5" drive, I would refer you to cloning the old drive onto the new drive. There are special enclosures for M.2-2280:
http://www.amazon.com/...B00KQ4LNJC
You can put a new M2-2280 drive into the enclosure and attach it USB 3.0.
Put cloning software on the SSD in the laptop
Clone the data which is a full copy including all hidden files from the existing storage in the laptop onto the new drive and then swap them.
It is possible to use an external flash type SSD through USB 3.0 but you can't install the drive into the laptop. If you first put the new M2 drive in the laptop it will have nothing on it and your operating system and all data will be on the M2 storage stick you pulled out.
The 2280 is the width. Three shown in the pic. That is like your internal drive.
Add: The 512GB Lenovo uses is specified here:
http://www.samsung.com/...7&iaId=831
Compatible ones should fit and work.