The first thing you'll need to do is
read through the watercooling sticky in order to understand the workings of a loop. Since the loop will have to be assembled and disassembled during the course of it's intended service lie, the second order of business would be to understand the choice of parts since they can either be aesthetically pleasing or functional or both. The last bit of advice would be to keep in mind of your budget and the form factor since going for a smaller case could dictate that the case is asking for a more custom level watercooling setup meaning more angled fittings due to oddly placed bends or limited spaces.
If you plan on adding on a full cover block to your GTX960, might want to add info to
EK's Cooling Configurator drop down menu and see if your card is compatible. Computers with non reference cards are the hardest to build a csutom watercoolling loop around since there are limited number manufacturers for full cover waterblocks and with the large number of SKU's on any particular GPU manufacturer's opt for making full cover blocks for cards that are popular.
One last advice, you may need to add about 100USD due to the fact that you're building in a cubed Matx case though when you take a few steps back and see how much you're allocating towards your watercooling endeavor it's nearly the same amount as your build's cost which in hindsight(+IMHO) isn't a worthwhile endeavor but a money pit. You'd be best served by going with a closed loop cooler for a third of the price or, better yet, air cooling for a fifth of the price.