Packing a road bike with traditional rim brakes is usually a pretty straight forward exercise. However more care and improvisation may be required when packing a bike with disc brakes.
I would recommend removing the disc rotors. It is by far the easiest option and all the issues you may encounter as discussed below will go away. However if you decide to leave the disc rotors in place please read on.
Bike Box Alan provide guidance on the options and I would recommend you look at their advice, but that aside I wanted to share my own experience with my Specialized Diverge.
The Diverge is a multi-terrain bike that looks like a regular road bike but has a bulky frame, fatter tyres, large discs and an over-sized cassette. I have packed this bike without issue on numerous occasions so if the Diverge fits then your road bike will.
Bike Box Alan recommend removing the discs and where this is not possible/practical discuss other options. However, all cyclists that have shared their own experience with me of packing wheels with discs have all packed their wheels into the lid of the box in exactly the same configuration as with non-disc brake wheels. Please click on this link for my experience of removing brake discs.
Below you will see the wheels packed with the discs facing into the box. For the front wheel I removed the thru axel cylinder, so I could use a smaller quick release skewer. The problem with using a longer one is that it will protrude through the other side of the lid, which is a potential issue during transit. I cover this on my how to pack page. The rear wheel is secured with a standard rear wheel quick release skewer. The wheel is secure, but not over tightened.
There are two obvious areas of concern. Firstly, potential damage to the front wheel disc or the rear tyre, and secondly damage to the front tyre from the cassette. In both cases as there is no pressure from the deflated tyres they will not be damaged and nor will they push into the discs. I add a bit of cloth of bubble wrap in the gaps to ensure there is no rubbing.
The next challenge is to make sure there is nothing in the base of the box that would push into the discs. There should be no problem with the disc on the front wheel as this is not so exposed and underneath will be the frame which is secured flat to the base of the box. For most bikes the handlebars should not prove an issue (see how the pink box is packed below) but with the Diverge I found that the handlebars secured in the default position had the potential to push into the disc of the rear wheel. I simply reversed the position and the issue was solved.
Something else I would recommend with disc brakes is to place a coin or bit of plastic between the pads and then wrap some tape around to hold it in place.
