Tips on shipping large sets (super star destroyer, 2001 Discovery ship)
I would suggest that you first ask the buyer what they would like. For example I would definitely prefer to get the set fully disassembled as I would like to build it from scratch.

If the buyer doesn't care which way you ship it, fully disassembled is still the safest way. It will take up less room and also it is less likely that parts will be damaged or warped in shipping. You can pack loose parts in ziplock bags.

If the buyer would like the set partially disassembled you can take it apart in the most logical sections, then first wrap each section in cellophane wrapping (the kind used for food). Cellophane protects an assembled set the best because it "sticks" to LEGO leaving little or no gaps, so parts won't fall off. Once you have done that, use bubble wrap around the sections to protect them from bumps while shipping, then place them in the box or boxes. 

Also, use FRAGILE stickers or stamps on the box. They do help. And make sure you buy full insurance to cover any loss or damage. Even if the buyer doesn't want to pay for it, it is worth it for your own peace of mind. Hope this helps some! ;)