Hi Kenny,
If you really want to look after your ski, then you have to either buy or make a suitable roof-rack with a cradle. What you need is something to spread the load as much as possible, and this includes for the material you use to tie down your boat (although, I wouldn`t go with nylon ropes). If you use normal tie-down straps, you should get the ones with wider sections to go where they contact with the boat, or use somethng else to disperse the pressure on the ski.
Also, try to locate your roof-racks as far apart as possible so that the wind will have less leverage on the ends and be less likely to twist it off your roof. Don`t forget to put a little red rag off the trailing end, so others can see it from behind and you can see it when reversing.
Thule do some good racks, so that could be your starting point.
Once you get a few scratches on your ski you might get a bit more casual about how you look after your ski, in which case you could follow my example in the photos from Facebook below:
www.facebook.com/profile.php?id=50842255...=156081&id=508422559
Happy paddling,
Owen