PCIe Prototyping Backplane
Looking through the datasheet it looks like the CC6678 can operate in root complex mode so you should be able to connect the two.   I did a similar board for testing a large batch of pcie cards.  

Lanes

If I were going to try it I'd start with a 4 layer board.  You're going to want nice 100Ohm differential pairs to connect your lanes together.   It only supports 1 or two of them so that shouldn't be a problem.  Just run them over a GND plane on layer two.  Just follow good practice here for routing HS signals. Oh and Tx -> Rx, and watch your polarities :)

Clock

I saw the clock generator you picked from your other post, I'd probably put a 1->2 fanout buffer and drive one to each of your pcie slots.

Reset

You're going to need to generate a reset pulse for the cards as usually the mother board would do that.  You could just slap down a simple supervisor that monitors 12V and tie it's reset output to both connectors.   Maybe add a pushbutton too so you can reset manually during debug.  I used a Linear LTC2916CDDB-1#TRMPBF.

Power

You're going to need 12V and 3.3V to power the connectors.  I just used a standard desktop pc power supply because I had a bunch and they're easy to get.  I just used a standard mother board power supply connector (Molex 44206-0007) and I put a little toggle switch from PS_ON to GND to turn things on and off.  Oh and throw in a few 100uF tantalums on each rail for good measure.

Don't be nervous keep the lanes short, match the impedances and you should be fine. 

Here's a pinout if you need one: